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References
Agalarov SC, Sridhar Prasad G, Funke PM, Stout CD, Williamson JR. Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science 2000; 288: 107–113.
Ahn AH, Kunkel LM. The structure and functional divergence of dystrophin. Nat Gen 1993; 3: 283–291.
Ahringer J, Kimble J. Control of the sperm-oocyte switch in Caenorrhabiditis elegans hermaphrodites by the fem-3 3’ untranslated region. Nature 1991; 349: 346–348.
Akerib CC, Meyer BJ. Identification of X chromosome regions in Caenorhabditis elegans that contain sex-determination signal elements. Genetics 1994; 138: 1105–1125.
Allain FH, Gubser CC, Hower PW, Nagai K, Neuhaus D, Varani G. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature 1996; 380: 646–650.
Allain FH, Gilbert DE, Bouvet P, Feigon J. Solution structure of the two N-terminal RNA-binding domains of nucleolin and NMR study of the interaction with its RNA target. J Mol Biol 2000; 303: 227–241.
Altman S. Kirsebom L, Talbot S. Recent studies of ribonuclease P. FASEB J 1993; 7: 7–14.
Altona C. Classification of nucleic acid junctions. J Mol Biol 1996; 263: 568–581.
Altuvia S, Weinstein-Fischer D, Zhang A, Postow L, Storz G. A small, stable RNA-induced by oxidative stress: role as a pleiotropic regulator and antimutator. Cell 1997; 90: 43–53.
Amarasinghe GK, De Guzman RN, Turner RB, Summers MF. NMR structure of stem-loop SL2 of the HIV-1 psi RNA packaging signal reveals a novelvA-U-A base-triple platform. J Mol Biol 2000; 299: 145–156.
Ambros V, Horvitz HR. Heterochronic mutants of the nematode Caenorhabditis elegans. Science 1984; 226: 409–416.
Ambros V, Moss EG. Heterochronic genes and the temporal control of C. elegans development. Trends Genet 1994; 10: 123–127.
Amrein H, Axel R. Genes expressed in neurons of adult male Drosophila. Cell 1997; 88: 459–469.
Andersen J, Delihas N, Ikenaka K, Gren PJ, Pines O, Ilercil O, Inouye, M. The isolation and characterization of RNA coded by the micF gene in Escherichia coli. Nucl Acids Res 1987; 15:2089–2101.
Andersen J, Forst SA, Zhao KJ, Inouye M, Delihas N. The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli. J Biol Chem 1989; 264: 17961–17970.
Andersson U, Antonicka H, Houstek J, Cannon B. A novel principle for conferring selectivity to poly(A)-binding proteins: interdepence of two synthase beta-subunit mRNA-binding proteins. Biochem J 2000; 346: Pt 1:33–39.
Andresson T, Ruderman JV. The kinase Eg2 is a component of the Xenopus oocyte progesteron-activated signaling pathway. EMBO J. 1998; 17: 5627–5637.
Ansel-McKinney P, Gehrke L. RNA determinants of a specific RNA-coat protein peptide interaction in alfalfa mosaic virus: conservation of homologous features in ilarvirus RNAs. J Mol Biol 1998;278:767–785.
Antes T, Costandy H, Mahendran R, Spottswood M, Miller D. Insertional editing of mitochondrial tRNAs of Physarum polycephalum and Didymium nig ripes. Mol Cell Biol 1998; 18: 7521–7527.
Ares M, Igel AH. Lethal and temperature-sensitive mutations and their suppressors identify an essential structural element in U2 small nuclear RNA. Genes Dev 1990; 4: 2132–2145.
Arn EA, Macdonald PM. Motors driving mRNA localization: new insights from in vivo imaging. Cell 1998; 95: 151–154.
Askari FK, McDonnell WM. Molecular medicine: antisense-oligonucleotide therapy. New Engl J Med 1996; 334: 316–318.
Atkin AL, Schenkman LR, Eastham M, Dahlseid JN, Lelivelt MJ, Culbertson MR. Relationship between yeast polyribosome and upf proteins required for nonsense mRNA decay. J Biol Chem 1997; 272: 22163–22172.
Autexier C, Greider CW. Telomerase and cancer: revisiting the telomere hypothesis. Trends BiochemSci 1996; 21: 387–391.
Avni D, Biberman Y, Meyuhas O. The 5’ terminal oligopyrimidine tract confers translational control on TOP mRNAs in a cell-type and sequence context-dependent manner. Nucl Acids Res 1997; 25: 995–1001.
Bachellerie J-P, Cavaillé J. Guiding ribose methylation of rRNA. Trends Bioch Sci 1997; 22: 257–261.
Bachellerie JP, Michot B, Nicoloso M. Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem Sci 1995; 20: 261–264
Balakin AG, Smith L, Fournier MJ. The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 1996; 86: 823–834.
Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the ribosomal subunit at 2.4 Â resolution. Science 2000; 289: 905–920.
Baron C, Boeck A. The length of the aminoacyl-acceptor stem of the selenocystein-specific tRNASer of Escherichia coli is the determinant for binding to elongation factor SELB or Tu. J Biol Chem 1991; 266. 20375–20379.
Baron C, Heider J, Boeck A. Interaction of translation factor SELB with the formate dehydrogenase H selenopolypeptide mRNA. PNAS 1993, 90. 4181–4185.
Barr ML, Bertram EG. A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar sattelite during accelerated nucleoprotein synthesis. Nature 1949; 163; 676–677.
Barth C, Greferath U, Kotsifas M, Fisher PR. Polycistronic transcription and editing of the mitochondrial small subunit (SSU) ribosomal RNA in Dictyostelium discoideum. Curr Genet 1999;36:55–61.
Bartolomei MS, Webber AL, Brunkow ME, Tilghman SM. Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Genes Dev 1993; 7: 1663–1673.
Bartolomei MS, Zemel S, Tilghman SM. Parental imprinting of the mouse HI9 gene. Nature 1991;351:153–155.
Basilio C, Wahba AJ, Lengyel P, Speyer JF, Ochoa S. Synthetic polynucleotides and amino acid code. PNAS 1962; 48: 613–616.
Bass BL. Physarum-C the difference. Nature 1991; 349: 370–371.
Bass BL. Splicing: the new edition. Nature 1991; 352: 283–284
Bass BL. An I for editing. Curr Biol 1995; 5: 598–600.
Baum CL, Teng BB, Davidson NO. Apolipoprotein B messenger RNA editing in the rat liver. Modulation by fasting and refeeding a high carbohydrate diet. J Biol Chem 1990; 265: 19263–19270.
Bektesh S, Van Doren K, Hirsch D. Presence of the Caenorhabditis elegans spliced leader on different mRNAs and in different genera of neamtodes. Genes Dev 1988; 2: 1277–1283.
Belfort M. Prokaryotic introns and inteins: a panoply of form and function. J Bacteriol 1995; 177: 3897–3903.
Belostotsky DA, Meagher RB. Different organ specifc expression of three poly(A) binding protein genes from Arabidopsis thaliana. PNAS 1993; 90:6686–6696.
Belsham GJ, Jackson RJ. Translation initiation on Picornavirus RNA. In: Sonenberg N, Hershey J, Mathews M (eds). Translational Control of Gene Expression, CSHL Press, 2000; 860–900.
Beltrame M, Henry Y, Tollervey D. Mutational analysis of an essential binding site for the U3 snoRNA in the 5’ external transcribed spacer of yeast pre-rRNA. Nucleic Acids Res 1994; 22: 5139–5147.
Beltrame M, Tollervey D. Identification and functional analysis of two U3 binding sites on yeast pre-ribosomal RNA. EMBO J 1992; 11: 1531–1542.
Beltrame M, Tollervey D. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J 1995; 14: 4350–4356.
Benne R. RNA editing: is there a message? Trends Genet 1990; 6: 177–181
Benne R. RNA editing. Ellis Horwood, 1993.
Benne R. The long and short of it. Nature 1996; 380: 391–392.
Benne R, Van den Burg J, Brakenhoff JP, Sloof P, Van Boom JH and Tromp MC. Major transcript of the frameshifted coxll gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 1986; 46: 819–826.
Berget SM, Moore C, Sharp PA. Spliced segments at the 5’ terminus of adenovirus 2 late mRNA. PNAS 1977; 74: 3171–3175.
Berglund JA, Chua K, Abovich N, Reed R, Rosbash M. The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell 1997; 89: 781–787.
Bergmann KF, Gerin JL. Antigens of hepatitis delta virus in the liver and serum of humans and animals. J Infect Dis 1986; 154: 702–706.
Bernus I, Mitchell AM, Manley SW, Mortimer RH. Lack of membrane transport of 1-thyroxine sulphate in the human choriocarcinoma cell line, JAr. Placenta. 2000; 21: 283–285.
Berry MJ. Recoding UGA as selenocysteine. In: Sonenberg N, Hershey J, Mathews M (eds). Translational Control of Gene Expression, CSHL Press 2000; 763–783.
Berry MJ, Banu L, Chen Y, Mandel SJ, Kieffer JD, Harney JW, Larsen PR. Recognition of UGA as a selenocysteine codon in Type I deiodiase requires sequences in the 3’ untranslated region. Nature 1991; 353: 273–276.
Beyer K, Dandekar T, Keller W. RNA-ligands selected by cleavage stimulation factor (CstF) contain distinct sequence motifs that function as downstream elements in 3’-end processing or pre-mRNA. J Biol Chem 1997; in press.
Bhat GJ, Koslowsky DJ, Feagin JE, Smiley BL, Stuart K. An extensively edited mitochondrial transcript in kinetoplastids encodes a protein homologous to ATPase subunit 6. Cell 1990; 61: 885–894.
Bhattacharyya A and Blackburn EH. A functional telomerase RNA swap in vivo reveals the importance of nontemplate RNA domains. PNAS 1997; 94: 2823–2827.
Binder S, Marchfelder A, Brennicke A, Wissinger B. RNA editing in trans-splicing intron sequences of nad2 mRNAs in Oenothera mitochondria. J Biol Chem 1992; 267: 7615–7623.
Binder S, Marchfelder A, Brennicke A. RNA editing of tRNA(Phe) and tRNA(Cys) in mitochondria of Oenothera berteriana is initiated in precursor molecules. Mol Gen Genet 1994; 244: 67–74.
Black AC, Ruland CT, Luo J, Bakker A, Fraser JK, Rosenblatt JD. Binding of nuclear proteins to HTLV-II cis-acting repressive sequence (CRS) RNA correlates with CRS function. Virology 1994; 200: 29–41.
Black DL, Chabot B, Steitz JA. U2 as well as Ul small nuclear ribonucleoproteins are involved in pre-messenger RNA splicing. Cell 1985; 42: 737–750.
Blackburn EH. Telomerase. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA World., CSHL Press 1999; 609–635.
Blackburn EH. The end of the (DNA) line. Nat Struct Biol 2000; 7: 847–850.
Blackburn EH, Gall JG. A tandemly repeated sequence at the termini of the extrachromosomal ribsomal RNA genes in Tetrahymena. J Mol Biol 1978; 120:33–53.
Blackburn EH, Greider CW. Telomere. Plainview, CSHL Press 1995.
Blasco MA, Funk W, Villeponteau B, Greider CW. Functional characterization and developmental regulation of mouse telomerase RNA. Science 1995; 269: 1267–1270.
Blum B, Bakalara N, Simpson L. A model for RNA editing in kinetoplastid mitochondria: “guide” RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 1990; 60: 189–198.
Blum B, Sturm NR, Simpson AM, Simpson L. Chimeric gRNA-mRNA molecules with oligo(U) tails covalently linked at sites of RNA editing suggest that U addition occurs by transesterification. Cell 1991; 65: 543–550.
Blumenthal T. Trans-splicing and polycistronic transcription in Caenorhabditis elegans. Trends Genet 1995; 11: 132–136.
Boelens WC, Jansen EJR, van Venrooij WJ, Stripecke R, Mattaj IW, Gunderson SI. The human Ul snRNP-specific UlA protein inhibits polyadenylation of its own pre-mRNA. Cell 1993; 72:881–892.
Bohnen L. Trans-splicing of pre-mRNA in plants, animals and protists. FASEB J 1993; 7: 40–46.
Bonino F, Heermann KH, Rizzetto M, Gerlich WH. Hepatitis delta virus: protein composition of delta antigen and its hepatitis B virus-derived envelope. J Virol 1986; 58: 945–950.
Bork P, Gibson TJ. Applying motif and profile searches. Methods Enzymol 1996; 266:162–184.
Borner GV, Mori M, Janke A Paabo S. RNA editing changes the identity of a mitochondrial tRNA in marsupials. Embo J 1996; 15:5949–5957.
Boros I, Posfai G, Venetianer P. High copy number derivatives of the plasmid cloning vector pBR322. Gene 1984; 30:257–260.
Böstrom K, Garcia Z, Poksay KS, Johnson DF, Lusis AJ, Innerarity TL. Apolipoprotein B mRNA editing. Direct determination of the edited base and occurrence in non-apolipoprotein B-producing cell lines. J Biol Chem 1990; 265: 22446–22452.
Bosquet-Antonelli C, Henry Y, Gélugne JP, Caizergues-Ferrer M, Kiss T. A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs. EMBO J 1997; in press
Boudvillain M, de Lencastre A, Pyle AM. A tertiary interaction that links active-site domains to the 5’ splice site of a group II intron. Nature 2000; 406:315–318.
Bousquet-Antonelli C, Presutti C, Tollervey D. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 2000; 102:765–775.
Bouthinon D, Soldano H. A new method to predict the consensus secondary structure of a set of unaligned RNA sequences. Bioinformatics 1999; 15: 785–798.
Brächet J. Reminiscences about nucleic acid cytochemistry and biochemistry. TIBS 1987; 12: 244–246.
Brand S, Bourbon HM. The developmentally regulated Drosophila gene rox8 encodes an RRM-type RNA-binding protein structure related to human TIA-1-type nucleolysins. Nucl Acids Res 1993; 21: 3699–3704.
Brandeis M, Kafri T, Ariel M, Chaillet JR, McCarrey J, Razin A, Cedar H. The ontogeny of allele-specific methylation associated with imprinted genes in the mouse. EMBO J 1993; 12: 3669–3677.
Brannan CI, Dees EC, Ingram RS, Tilghman SM. The product of the HI9 gene may function as an RNA. Mol Cell Biol 1990; 10: 28–36.
Braun RE. Temporal control of protein synthesis during spermatogenesis. Int J Androl 2000; 23 Suppl 2:92–94.
Brehm K, Jensen K, Frosch M. mRNA Trans-splicing in the Human Parasitic Cestode Echinococcus multilocularis J Biol Chem 2000; 275: 38311–38318.
Breitwieser W, Markussen FH, Horstmann H, Ephrussi A. Oskar protein interaction with Vasa represents an essential step in polar granule assembly. Genes Dev 1996; 10: 2179–2188.
Brenner S, Jacob F, Meselson M. An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature 1961; 190:576–581.
Brockdorff N, Ashworth A, Kay GF, McCabe VM, Norris DP, Cooper PJ, Swift S, Rastan S. The product of the mouse XIST gene is a 15 kb inactive X-specific transcript containing no conserved ORF and is located in the nucleus. Cell 1992; 71: 515–526.
Brow DA, Guthrie C. Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature 1988; 334: 213–218.
Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, Willard HF. A gene from the region of the human X-inactivation centre is expressed exclusively from the inactive X chromosome. Nature 1991; 349: 38–44.
Brown BD, Goldstein. Teaching old dogmas new tricks. Nature 1987; 330: 113–114.
Brown CJ, Hendrich BD, Rupert JL, Lafreniere RG, Xing Y, Lawerence J, Willard H. The human XIST gene: Analysis of a 17kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 1992; 71: 527–542.
Brown CY, Mize GJ, Pineda M, George DL and Morris DR. Role of two upstream open reading frames in the translational control of oncogene mdm2. Oncogene 1999; 18: 5631–5637.
Brown BD, Zipkin ID, Harland RM. Sequence-specific endonucleolytic cleavage and protection of mRNA in Xenopus and Drosophila. Genes Dev 1993; 7: 1620–1631.
Brunak S, Engelbrecht J. Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level. Proteins 1996; 25:237–252.
Brunkow M, Tilghman SM. Ectopic expression of the H19 gene in mice causes prenatal lethality. Genes Dev 1991; 5: 1092–1101.
Bruzik JP, Maniatis T. Spliced leader RNAs from lower eukaryotes are trans-spliced in mammalian cells. Nature 1992; 360: 692–695.
Bruzik JP, Steitz JA. Spliced leader RNA sequences can substitute for the essential 5’ end of Ul RNA during splicing in a mammalian in vitro system. Cell 1990; 62: 889–899
Buettner C, Harney JW, Berry MJ. The Caenorhabditis elegans homologue of thioredoxin reductase contains a selenocysteine insertion sequence (SECIS) element that differs from mammalian SECIS elements but directs selenocysteine incorporation. J Biol Chem 1999; 274:21598–21602.
Buiting K, Saitoh S, Gross S, Dittrich B, Schwartz S, Nicholls R, Horsthemke B. Inherited microdeletions in the Angelman and Prader-Willi syndromes define an imprinting centre on human chromosome 15. Nat Genet 1995; 9: 395–400.
Bürge CB, Tuschl T, Sharp PA. Splicing of precursors to mRNAs by the spliceosome. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA World, CSHL Press 1999; 525–560.
Burke DH, Gold L. RNA aptamers to the adenosine moiety of S-adenosyl methionine: structural inferences from variations on a theme and the reproducibility of SELEX. Nucleic Acids Res 1997; 25:2020–2024.
Burtis KC, Baker BS. Drosophila doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides. Cell 1989;56,997–1010.
Caffarelli E, Fragapane P, Ghering C, Bozzoni I. THe accunmulation of mature RNA for the Xenopus laevis ribosomal protein LI is controlled at the level of splicing and turnover of the precursor RNA. EMBO J 1987; 6: 3492–3498.
Camaschella C, Zecchina G, Lockitch G, Roetto A, Campanella A, Arosio P, Levi S. A new mutation (G51C) in the iron-responsive element (IRE) of L-ferritin associated with hyperferritinaemia-cataract síndrome decreases the binding affinity of the mutated IRE for iron-regulatory proteins. Br J Haematol 2000; 108: 480–482.
Canete-Soler R, Schlaepfer WW. Similar poly(C)-sensitive RNA-binding complexes regulate the stability of the heavy and light neurofilament mRNAs. Brain Res 2000; 867: 265–279.
Caponigro G, Mühlrad D, Parker R. A small segment of the MAT alpha 1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role of rare codons. Mol Cell Biol 1993;13:5141–5148.
Caponigro G, Parker R. mRNA turnover in yeast promoted by the MATalphal instability element. Nucleic Acid Res 1996; 24: 4304–4312.
Carballo E, Lai WS, Blackshear PJ. Feedback inhibition of macrophage tumor necrosis factor-alpha production by tristetraprolin. Science 1998; 281: 1001–1005.
Carrara G, Calandra P, Fruscoloni P, Tocchini-Valentini GP. Two helices plus a linker: a small model substrate for eukaryotic RNase P. PNAS 1995; 92. 2627–2631.
Carstens RP, Wagner EJ, Garcia-Blanco MA. An intronic splicing silencer causes skipping of the IIIb exon of fibroblast growth factor receptor 2 through involvement of polypyrimidine tract binding protein. Mol Cell Biol 2000; 20:7388–7400.
Carter MS, Kuhn KM, Sarnow P. Cellular internal ribosome entry site elements and the use of cDNA microarrays in their investigation. In: Sonenberg N, Hershey JWB, and Mathews MB (eds) Translational ControL, CSHL PRESS 2000; 615–635.
Casey JL, Bergmann KF, Brown TL, Gerin JL. Structural requirements for editing in hepatitis d virus: evidence for a uridine-to-cytidine editing mechanism. Proc Natl Acad Sci USA 1992; 89: 7149–7153.
Casey JL, Hentze MW, Koeller DM, Caugham SW, Rouault TA, Klausner RD, Harford JB. Iron-responsive elements: regulatory RNA sequences that control mRNA levels and translation. Science 1998; 240: 924–928.
Castanotto D, Rossi J. Sarver N. Antisense cataltyic RNAs as therapeutic agents. Adv Pharmacol 1994; 25: 289–317.
Cavaillé J, Nicoloso M, Bachellerie J-P. Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 1996; 383: 732–735.
Cech TR. Ribozymes and their medical implications. J Am Med Assoc 1988; 260: 3030–3034.
Cech TR. Structure and mechanisms of the large catalytic RNAs: groupl and group II introns and ribonuclease P. In: Gesteland RF, Atkins JF (eds), The RNA World, CSHL Press 1993; 239–269.
Cech TR. Structural biology. The ribosome is a ribozyme. Science 2000; 289:878–879.
Cech TR and Golden BL. Building a catalytic active site using only RNA. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA World, CSHL Press 1999; 321–349.
Chadalavada DM, Knudsen SM, Nakano S, Bevilacqua PC. A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. J Mol Biol 2000;301:349–367.
Chambón P. Split genes. Sci Am 1981; 244: 60–71.
Chang BJ, Lau P, Chan L. Apolipoprotein B mRNA editing. In: Grosjean H, Benne R (eds). Modification and Editing of RNA 1998, 325–342.
Chang FL, Chen PJ, Tu SJ, Wang CJ, Chen DS. The large form of hepatitis d antigen is crucial for assembly of hepatitis d virus. PNAS 1991; 88: 8490–8494.
Chang KY, Tinoco I, Jr. The structure of an RNA hairpin complex of the HIV TAR hairpin loop and its complement. J Mol Biol 1997; 269: 52–66.
Chao M, Hsieh SY, Taylor J. Role of two forms of the hepatitis delta virus antigen: evidence for a mechanism of self-limiting genome replication.J Virol 1990; 64: 5066–5069.
Chapdelaine Y, Bohnen L. The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a frans-splicing model for this gene-in-pieces. Cell 1991; 65: 465–472.
Chapon C, Cech TR, Zaug AJ. Polyadenylation of telomerase RNA in budding yeast. RNA 1997; 3: 1337–1351.
Chen CY, Xu N, Shyu AB. mRNA decay mediated by two distinct AU-rich elements from c-fos and granulocyte macrophage colony-stimulating factor transcripts: Different deadenylation kinetics and uncoupling from translation. Mol Cell Biol 1995; 15: 5777–5788.
Chen CY, Del Gatto-Konczak F, Wu Z, Karin M. Stabilization of interleukin-2 mRNA by the c-Jun NH2-terminal kinase pathway. Science 1998; 280: 1945–1949.
Chen JL, Blasco MA, Greider CW Secondary structure of vertebrate telomerase RNA. Cell 2000; 100 503–514.
Chen J-H, Le S-Y, Maizel J. A procedure for RNA pseudoknot prediction. Comp Appl Biosci 1992; 8: 243–248.
Chen S-H, Habib G, Yang C-Y, Gu Z-W, Lee BR, Weng S-A, Silbermann SR, Cai S-J, Deslypere JP; Rosseneu M, Gotto JR AM, Li W-H, Chan L. Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science 1987; 238: 363–366.
Chiba Y, Ishikawa M, Kijima F, Tyson RH, Kim J, Yamamoto A, Nambara E, Leustek T, Wallsgove RM, Naito S. Evidence for autoregulation of cystathione gamme-synthase mRNA stability in Arabidopsis. Science 1999; 286:1371–1374.
Choo Y, Sánchez-Garcia I, Klug A. In vivo represssion by a site-specific DNA-binding protein designed against an oncogenic sequence. Nature 1994; 372: 642–645.
Chou JH, Greenberg JT, Demple B. Posttranscriptional repression of Escherichia coli OmpF protein in response to redox stress: postive control of the micF antisense RNA by the soxRS locus. J Bacteriol 1993; 175: 1026–1031.
Chow LT, Gelinas RE, Broker TR, Roberts RJ. An amazing sequence arrangement at the 5’ ends of adenovirus 2 messenger RNA. Cell 1977; 12: 1–8.
Chu E et al. Autoregulation of human thymidilate synthase messenger RNA translation by thymidilate synthase. PNAS 1991; 8: 8977–8981.
Chu S, Archer RH, Zengel JM and Lindahl L. The RNA of RNase MRP is required for normal processing of ribosomal RNA. PNAS 1994; 91: 659–663.
Clark RE. Poor cellular uptake of antisense oligodeoxynucleotides: an obstacle to their use in chronic myeloid leukaemia. Leuk Lymphoma 1995; 19: 189–195.
Clemson CM, McNeil JA, Willard H, Lawerence JB. XIST paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J Cell Biol 1996;132: 1–17.
Cohen SP, McMurray LM, Levy SB. mar A locus causes decreased expression of OmpF porin in multiple-antibiotic-resistant (Mar) mutants of Escherichia coli. J Bacteriol 1988; 170: 5416–5422.
Coles H. Nobel panel rewards prion theory after years of heated debate. Nature 1997; 389: 529.
Colomer R, Lupu R, Bacus SS, Gelmann EP. erbB-2 antisense oligonucleotides inhibt the proliferatin of breast cancer carcinoma cells with erbB-2 oncogene amplification. Br. J. Cancer 1994; 70: 819–825.
Conn GL, Draper DE, Lattman EE, Gittis AG. Crystal structure of a conserved ribosomal protein-RNA complex. Science 1999; 284: 1171–1174.
Conrad R, Thomas J, Spieth J, Blumenthal T. Insertion of part of an intron into the 5’ untranslated region of a Caenorhabditis elegans gene converts it into a trans-spliced gene. Mol Cell Biol 1991; 11: 1921–1926.
Constancia M, Dean W, Lopes S, Moore T, Kelsey G, Reik W. Deletion of a silencer element in igf2 results in loss of imprinting independent of HI 9. Nat Genet 2000; 26: 203–206.
Cooper JP, Nimmo ER, Allshire RC, Cech T. Regulation of telomere length and function by a myb-domain protein in fission yeast. Nature 1997; 385: 744–747.
Copeland PR; Fletcher JE, Carlson BA, Hatfield DL, Driscoll DM. A novel RNA binding protein, SPB2, is required for the translation of mammalian selenoprotein mRNAs. EMBO J 2000; 19: 306–314.
Costa M, Dème E, Jacquier A, Michel F. Multiple tertiary interactions involving domain II of group II self-splicing introns. J Mol Biol 1997; 267: 520–536.
Coughlin BC, Teixeira SM, Kirchhoff LV, Donelson JE. Amastin mRNA abundance in Trypanosoma cruzi is controlled by a 3’-untranslated region position-dependent cis-element and an untranslated region-binding protein. J Biol Chem 2000; 275: 12051–12060.
Covello PS, Gray MW. RNA editing in plant mitochondria. Nature 1989; 341: 662–666.
Covello PS, Gray MW. RNA sequence and the nature of the Cu-binding site in cytochrome c oxidase. FEBS Lett 1990; 268: 5–7.
Covello PS, Gray MW. Silent mitochondrial and active nuclear genes for subunit 2 of cytochrome c oxidase (cox2) in soybean: evidence for RNA-mediated gene transfer. EMBO J 1992; 11: 3815–3820
Cox TC, Bawden MJ, Martin A, May BK. Human erythroid 5-aminolevulinate synthase: promoter analysis and identification of an iron-responsive element in the mRNA. EMBO J 1991; 10: 1891–1902.
Crick FHC. The genetic code. Cold Spring Harbor Symp Quant Biol. 1965; 31.
Crick FHC. The central dogma of molecular biology. Nature 1970; 227: 561–563.
Crick FHC. Split genes and RNA splicing. Science 1979; 204: 264–271.
Culbertson MR. RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet 1999; 15: 74–80.
Cullen BR. RNA-sequence-mediated gene regulation in HIV-1. Infect Agents Dis 1994; 3: 68–76.
Cullen BR, Malim MH. The HIV-1 Rev protein: prototype of a novel class of eukaryotic post-transcriptional regulators. TIBS 1991; 16: 346–350.
Culver GM, Cate JH, Yusupova GZ, Yusupova MM, Noller HF. Indentification of an RNA-protein bridge spanning the ribosomal subunit interace. Science 1999; 285: 2133–2136.
Currey KM, Shapiro BA. Secondary structure computer prediction of the poliovirus 5’ noncoding region is improved by a genetic algorithm. CABIOS 1997; 13: 1–12.
Czaplinski K, Ruiz-Echevarria MJ, Gonzalez CI, Peltz SW. Should we kill the messenger? The role of the surveillance complex in translation termination and mRNA turnover. Bioessays 1999;21:685–696.
Dabeva MD, Post-Beitenmiller MA, Warner JR. Autogenous regulation of splicing of the transcript of a yeast ribosomal protein gene. Proc Natl Acad Sci USA 1986; 83:5854–5857.
Dabiri GA, Lai F, Drakas RA, Nishikura K. Editing of the GluR-B ion channel RNA in vitro by recombinant double-stranded RNA adenosine deaminase. EMBO J 1996; 15: 34–45.
Dalmay T, Hamilton A, Rudd S, Angelí S, Baulcombe DC. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 2000; 101: 543–53.
Dandekar T. Yeast U3 localization and correct sequence (snR17a) and promotor activity (snR17b) identified by homology search. DNA-Sequence. 1991; 1: 217–218
Dandekar T, Argos P. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted a-helices: Crystal structure of the protein DNA-complex (commentary). Chemtracts 1993; 4: 62–65.
Dandekar T, Argos V. ln vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence (commentary). Chemtracts 1995; 5: 314–316.
Dandekar T, Argos P. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily (commentary). Chemtracts 1995; 5: 324–325.
Dandekar T, Argos P. Selection of RNA-binding peptides in vivo (commentary). Chemtracts 1996; 6. 107–110.
Dandekar T, Argos P. Determination of the fold of the core protein of hepatitis B virus by electron cryomicroscopy (commentary). Chemtracts 1998; 11: 161–165.
Dandekar T, Hentze MW. Finding the hairpin in the haystack: Searching for RNA motifs. Trends Genetics 1995; 11: 45–50.
Dandekar T, Koch G. DNA and mRNA sequence of the immune protective DNA ligase I gene match the rev response element of HIV. DNA Sequence—the Journal of DNA sequencing and mapping 1996; 6: 119–121.
Dandekar T, Ribes V, Tollervey D. Schizosaccharomyces pombe U4 small nuclear RNA closely resembles vertebrate U4 and is required for growth. Journal of Molecular Biology 1989; 208:371–379.
Dandekar T, Sharma K. Regulatory RNA. Springer Verlag Berlin Heidelberg New York 1998.
Dandekar T., Sibbald PR. Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates. Nucleic Acids Res 1990; 18: 4719–4726.
Dandekar T, Tollervey D. Cloning of Schizosaccharomyces pombe genes encoding the U1,U2,U3 and U4 snRNAs. Gene 1989; 81: 227–235.
Dandekar T, Tollervey D. 33 nucleotides including the TATA box are both necessary and sufficient for U2 transcription in Schizosaccharomyces pombe. Molecular Microbiology 1991;5: 1621–1625.
Dandekar T, Tollervey D. Mutational analysis of Schizosaccharomyces pombe U4 snRNA by plasmid exchange. Yeast 1992; 8: 647–653.
Dandekar T,.Tollervey D. Identification and functional analysis of a novel yeast small nucleolar RNA. Nucleic Acids Res 1993; 21: 5386–5390.
Dandekar T, Stripecke R, Gray NK, Goosen B, Constable A, Johansson HE, Hentze MW. Identification of a novel iron-responsive element in murine and human erythroid delta-aminolevulinic acid synthase mRNA. EMBO J 1991; 10: 1903–1909.
Dandekar T, Beyer K, Bork P, Kenealy MR, Pantopoulos K, Hentze M, Sonntag-Buck V, Flouriot G, Gannon F, Schreiber S. Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches. Bioinformatics 1998; 14: 271–278.
Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sanchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P. Re-annotating the mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res 2000; 28: 3278–3288.
Davidson NO, Powell LM, Wallis SC, Scott J. Thyroid hormone modulates the introduction of a stop codon in rat liver apolipoprotein B messenger RNA. J Biol Chem 1988; 263: 13482–13485.
Decker CJ, Parker R. Mechanisms of mRNA degradation in eucaryotes. TIBS 1994; 19: 336.
Decker CJ, Parker R. Diversity of cytoplasmic functions for the 3’ untranslated region of eukaryotic transcripts. Curr Opin Cell Biol 1995; 7: 386–392.
Deckman IC, Draper DE. S4-alpha mRNA translation regulation complex. II. Secondary structure of the RNA regulatory site in the presence and absence of S4. J Mol Biol 1987; 196: 323–332.
De Guzman RN, Wu ZR, Stalling CC, Pappalardo L, Borer PN, Summers MF. Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element. Science 1998; 279: 384–388.
de Lange T. Activation of telomerase in a human tumor. PNAS 1994; 91: 2882–2885.
Delbecq P, Werner M, Feller A, Filipowski RK, Messenguy F, Pierard A. A segment of mRNA encoding the leader peptide of CPAl gene confers repressin by arginine on a heterologuos yeast gene transcript. Mol Cell Biol 1994; 14: 2378–2390.
Delihas N. Regulation of gene expression by trans-encoded antisense RNAs. Mol Microbiol 1995;15:411–414.
De Los Santos T, Schweizer J, Rees CA, Francke U. Small evolutionary conserved RNA, resembling C/D box small nucleolar RNA, is transcibed from PWCRl, a novel imprinted gene in the Prader-Willi deletition region, which is highly expressed in brain. Am J Hum Genet 2000; 67: 1067–1082.
DeRosier DJ. Who needs crystals anyway? Nature 1997; 386: 26–27.
Devereux J, Haeberli P, Smithies O. A comprehensive sequence analysis package for the VAX. Nucleic Acids Res 1984; 12: 387–395.
Dichtl B, Tollervey D. Pop3 is essential for the activity of the RNAse MRP and RNAse P ribonucleoproteins in vivo. EMBO J 1997; 16: 417–429.
Dickson K.S, Bilger A, Ballantyne S, Wickens MP. The cleavage and polyadenylation specificity factor in Xenopus leavis oocytes is a cytoplasmic factor involved in regulated polyadenylation. Mol Cell Biol 1999; 19: 5707–5717.
Dieci G, Percudani R, Giuliodori S, Bottarelli L, Ottonello S. TFIIIC-independent in vitro transcription of yeast tRNA genes. J Mol Biol 2000; 299: 601–613.
Diwa A, Bricker AL, Jain C, Belasco JG. An evolutionary conserved RNA stem-loop functions as a sensors that directs feedback regulation of RNase E gene expression. Genes Dev 2000; 14: 1249–1260.
Dix DJ, Lin PN, McKenzie AR, Waiden WE, Theil EC. The influence of the base-paired flanking region on structure and function of the iron regulatory element. J Mol Biol 1993; 231:230–240.
Domeier ME, Morse DP, Knight SW, Portereiko M, Bass BL, Mango SE. A link between RNA interference and nonsense-mediated decay in Caenorhabditis elegans. Science 2000; 289:1928–1931.
Domier LL, McCoppin NK, D’Arcy CJ. Sequence requirements for translation initiation of Rhopalosiphum padi virus ORF2. Virology 2000; 268: 264–271.
Dominski Z, Marzluff WF. Formation of the 3’end of histone mRNA. Gene 1999; 239: 1–14.
Doolittle RF. (ed) Molecular evolution: computer analysis of protein and nucleic acid sequences. Methods in enzymology vol. 183. Academic Press, San Diego, 1990.
Doolittle WF. Phylogenetic classification and the universal tree. Science 1999; 284: 2124–2129.
Doudna JA, Grosshans C, Gooding A, Kundrot CE. Crystallization of ribozymes and small RNA motifs by a sparse matrix approach. PNAS 1993; 90: 7829–7833.
Doye V, Hurt EC. Genetic approaches to nuclear pore structure and function. Trends Genet. 1995; 11: 193–199.
Draper DE. Translation regulation of ribosomal proteins in E.coli. In: Ilan J (ed) Translational regulation of gene expression. Plenum Press New York, 1–25.
Draper DE. Protein-RNA recognition. Annu Rev Biochem 1995; 64: 593–620.
Dreyfuss G, Matunis MJ, Piñol-Roma S, Burd CG. hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 1993; 62:289–321.
Duarte CM, Pyle AM. Stepping through an RNA structure: A novel approach to conformational analysis. J Mol Biol 1998; 284: 1465–1478.
Duncker BP, Koops MD, Walker VK, Davies PL. Low temperature persistence of type I antifreeze protein is mediated by cold-specific mRNA stability. FEBS 1995; 377:185–188.
Dzau VJ, Mann MJ, Morishita R, Kaneda Y. Fusigenic viral liposome for gene therapy in cardiovascular diseases. PNAS 1996; 93: 11421–11425.
Ebeling S, Kundig C, Hennecke H. Discovery of a rhizobial RNA that is essential for symbiotic root nodule development. J Bacteriol 1991; 173: 6373–6382.
Ecker DJ, Vickers TA, Bruice TW. Pseudo-half-knot formation with RNA. Science 1992; 257: 958–961.
Eddy SR, Durbin R. Nucí Acids Res 1994; 22: 2079–2088.
Eden S, Cedar H Action at a distance. Nature 1995; 375: 16–17.
Egebjerg J, Kakekov V, Heinemann SF. Intron sequence directs RNA editing of the glutamate receptor subunit GluR2 coding sequence. PNAS 1994; 91: 10270–10274.
Ehricht R, Ellinger T, McCaskill JS. Cooperative amplification of templates by cross-hybridization (CATCH). Eur J Biochem 1997; 243: 358–364.
Eichler DC, Craig N. Processing of eukaryotic ribosomal RNA. Progr Nucl Acid Res Mol Biol 1994; 49: 197–239.
Endo T, Nadal-Ginard B. Three types of mucscle-specific gene expression in fusion-blocked rat skeletal muscle cells: Translational control in EGTA-treated cells. Cell 1987; 49: 515–526.
Ephrussi A, Lehmann R. Oskar induces germ cell formation. Nature 1992; 358:387–392.
Erard M, Barker DG, Amalric F, Jeang KT, Gatignol A. An Arg/Lys-rich core peptide mimics TRBP binding to the HIV-1 TAR RNA upper-stem/loop. J Mol Biol 1998; 279: 1085–1099.
Erdélyi M, Michon A-M, Guichet A, Bogucka-Glotzer J, Ephrussi A. A requirement for Drosophila cytoplasmic tropomyosin in oskar mRNA localization. Nature 1995; 377: 524–527.
Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL. Prediction of transcription terminators in bacterial genomes. J Mol Biol 2000; 301: 27–33.
Estevez AM, Simpson L. Uridine insertion/deletion RNA editing in trypanosome mitochondria-a review. Gene 1999; 240: 247–260.
Etzold T, Ulyanov A, Argos P. SRS: information retrieval system for molecular biology data banks. Methods Enzymol 1996; 266: 114–128.
Eul J, Graessmann M, Graesmann A. rrans-splicing and alternative-tandem-cis-splicing: two ways by which mammalian cells generate a truncated SV40 T-antigen. Nucleic Acids Res 1996; 24: 1653–1661.
Fabbri S, Fruscoloni P, Bufardeci E, Di Nicola Negri E, Baldi MI, Attardi DG, Mattoccia E, Tocchini-Valentini GP. Conservation of substrate recognition mechanisms by tRNA splicing endonucleases. Science 1998; 280:284–286.
Fabre E, Boelens WC, Wimmer C. Nupl45p is required for nuclear export of mRRNA and binds homopolymeric RNA in vitro via a novel conserved motif. Cell 1994; 78: 275–289.
Fabrizio P, Abelson J. Two domains of yeast U6 small nuclear RNA required for both steps of nuclear precursor messenger RNA splicing. Science 1990; 250: 404–409.
Farabaugh PJ, Qian Q, Stahl G. Programmed translational frame shifting, hopping, and readthrough of termination codons. In: Sonenberg N, Hershey JWB, Mathews MB (eds) Translational Control. CSHL Press 2000; 741–761.
Faubladier M, Cam K, Bouche J-P. Escherichia coli cell division inhibitor DicF-RNA of the dicB operon. J Mol Biol 1990; 212: 461–471.
Feagin JE, Stuart JM. Developmental aspects of uridine addition within mitochondrial transcripts of Trypanosoma brucei. Mol Cell Biol 1988; 8: 1259–1265.
Feagin JE, Jasmer DP, Stuart K. Developmentally regulated addition of nucleotides within apocytochrome b transcripts in Trypanosoma brucei. Cell 1987; 49: 337–345.
Fedor MJ. Structure and function of the hairpin ribozyme. J Mol Biol 2000; 297:269–291.
Felip E, Del-Campo JM, Rubio D, Vidal MT, Colomer R, Bermejo B. Overexpression of c-erbB-2 in epithelial ovarian cancer, prognostic value and relationship with response to chemotherapy. Cancer 1995; 75: 2147–2152.
Feng J, Funk W, Wang S., Weinrich SL, Avilion AA, Chiu CP, Adams R.R, Chang E, Allsopp R, Yu S, Le S, West D, Harley CB, Andrews WH, Greider CW, Villeponteau B. The RNA component of human telomerase. Science 1995; 269: 1236–1241.
Ferguson KC, Heid PJ, Rothman JH. The SLl trans-spliced leader RNA performs an essential embryological function in Caenorhabditis elegans that can also be supplied by SL2 RNA. Genes Dev 1996; 10:1543–1556.
Ferguson-Smith AC, Sasaki H, Cattanach BM, Surani MA. Parental-origin-specific epigenetic modification of the mouse H19 gene. Nature 1993; 362: 751–755.
Ferrandon D, Elphick L, Nüsslein-Volhard C, St Johnston D. Staufen protein associates with the 3’UTR of bicoid mRNA to form particles that move in a microtubule-dependent manner. Cell 1994;79:1221–1232.
Ferre-D’Amare AR, Zhou K, Doudna JA. A general module for RNA crystallization. J Mol Biol 1998a; 279: 621–631.
Ferre-D’Amare AR, Zhou K, Doudna JA. Crystal structure of a hepatitis delta virus ribozyme. Nature 1998b; 395: 567–574.
Fey J, Tomita K, Bergdoll M, Marechal-Drouard L. Evolutionary and functional aspects of C-to-U editing at position 28 of tRNA(Cys) (GCA) in plant mitochondria. RNA 2000; 6: 470–474.
Fichant GA, Burks C. Identification of potential tRNA genes in genomic DNA sequences. J Mol Biol 1991; 220:659–671.
Flach J, Bossie M, Vogl J, Corbett A, Jinks T, Williams DA, Silver PA. A yeast RNA-binding protein shuttles between the nucleus and the cytoplasm. Mol Cell Biol 1994; 14: 8399–8407.
Fontana W, Schuster P. Continuity in evolution: on the nature of transitions. Science 1998; 280: 1451–1455.
Forchhammer K, Leinfelder W, Boeck A. Identification of a novel translation factor necessary for the incorporation of selenoysteine into protein. Nature 1989; 342: 453–456.
Forlan N, Martegan E, Alberghina L. Post transcriptional regulation of MET2 gene of S.cerevisiae. Biochem Biophys Acta 1991; 1089: 47–53.
Fox CA, Sheets MD, Wickens MP. Poly(A) addition during maturation of frog oocytes: distinct nuclear and cytoplasmic activities and regulation by the sequence UUUUUAU. Genes Dev 1989;3:2151–2162.
Franch T, Petersen M, Wagner EG, Jacobsen JP, Gerdes K. Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure. J Mol Biol 1999; 294: 1115–1125.
Fritz CC, Zapp ML, Green MR. A human nucleoporin like protein that specifically interacts with HivRev. Nature 1995; 376: 530–533.
Gan W, Rhoads RE. Internal initiation of translation directed by the 5’ untranslated region of the mRNA for eIF4G, a factor involved in the picornavirus-induced switch from cap-dependent to internal initiation. J Biol Chem 1996; 271: 623–626.
Gan W, LaCelle M, Rhoads RE. Functional characterization of the internal ribosome entry site of eIF4G mRNA. J Biol Chem 1998; 273: 5006–5012.
Ganot P, Bortolin M-L, Kiss T. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 1997; 89: 799–809.
Garcia-Barrio MT, Naranda T, Vazquez-de-Aldana CR, Cuesta R, Hinnebusch AG, Tamame M. GCDIO, a translational repressor of GCN4, is the RNA-binding subunit of eukaryotic initiation factor-3. Genes Dev 1995; 9: 1781–1796.
Gaspin C, Cavaille J, Erauso G, Bachellerie JP. Archeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. J Mol Biol 2000; 297: 895–906.
Gautheret D, Cedergren RJ. Modeling the three dimensional structure of RNA using discrete nucleotide conformation sets. Mol Biol 1993; 229: 1049–1064.
Gay DA, Sisodia SS, Cleveland DW. Autoregulatory control of beta-tubulin mRNA stability is linked to translation elongation. PNAS 1989; 86: 5763–5767.
Geballe AP, Spaete RR, Mocarski ES. A cis-acting element within the 5’leader of a cytomegalovirus ß transcript determines kinetic class. Cell 1986; 46: 865–872.
Gebauer F, Richter JD. Cloning and characterization of a Xenopuspoly(A) polymerase. Mol. Cell. Biol. 1995; 15: 1422–1430.
Gebauer F, Corona DFV, Preiss T, Becker PB, Hentze MW. Translational control of dosage compensation in Drosophila by sex-lethal: cooperative silencing via the 5’ and 3’UTRs of msl-2 mRNA is independent of the poly(A) tail. EMBO J 1999; 18: 6146–6154.
Gebauer F, Merendino L, Hentze MW, Valcarcel J. Novel functions for nuclear factors in the cytoplasm: the Sex-lethal paradigm. Semin Cell Dev Biol 1997; 8: 561–566.
Gesteland RF, Atkins JF (eds). The RNA World. 1993; CSHL Press.
Gesteland RF, Cech TR, Atkins JF (eds). The RNA World. 1999; CSHL Press.
Ghisolfi-Nieto L, Joseph G, Puvion-Dutilleul F, Amalric F, Bouvet P. Nucleolin is a sequencespecific RNA-binding protein: characterization of targets on pre-ribosomal RNA. J Mol Biol 1996; 260: 34–53.
Giddings MC, Matveeva OV, Atkins JF, Gesteland RF. ODNBase-a web database for antisense oligonucleotide effectiveness studies. Bioinformatics 2000; 16: 843–844.
Gilbert W, de Souza SJ. Introns and the RNA world. In: Gesteland RF, Cech TR, Atkins JF (eds.) The RNA World. 1999; CSHL Press: 221–231.
Gilley D, Blackburn EH. The telomerase RNA pseudoknot is critical for the stable assembly of a catalytically active ribonucleoprotein. PNAS 1999; 96: 6621–6625.
Gilmartin GM, Fleming ES, Oetjen J, Graveley BR. CPSF recognition of an HIV-1 mRNA 3’-processing enhancer: multiple sequence contacts involved in poly(A) sited definition. Genes Dev 1995; 9: 72–83.
Gingras AC. Raught B, Sonenberg N. eIF4 initiation factors: effectors of mRNA recruitment to ribosomes and regulators of translation. Annu Rev Biochem 1999; 68: 913–963.
Girard JP, Lehtonen H, Caizergues-Ferrer M, Amalric F, Tollervey D, Lapeyre B. GARl is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J 1992; 11: 673–682.
Giuliano F, Arrigo P, Scalia F, Cardo PP, Damiani G. Potentially functional regions of nucleic acids recognized by a Kohonen’s self-organizing map. Comput Appl Biosci 1993; 9: 687–693.
Glenn JS, White JM. trans-dominant inhibition of human hepatitis delta virus genome replication. J Virol 1991; 65: 2357–2361.
Gohlmann HW, Weiner J 3rd, Schon A, Herrmann R. Identification of a small RNA within the pdh gene cluster of Mycoplasma pneumoniae and Mycoplasma genitalium. J Bacteriol 2000; 182: 3281–3284.
Golden BL, Gooding AR, Podell ER, Cech TR. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 1998; 282: 259–264.
Goldschmidt-Clermont M, Choquet Y, Girard-Bascou J, Michel F, Schirmer-Rahire M, Rochaix JD. A small chloroplast RNA may be required for trans-splicing in Chlamydomonas reinhardtii. Cell 1991; 65: 135–143.
Golightly LM, Mbacham W, Daily J, Wirth DF. 3’UTR elements enhance expression of Pgs28, an ookinete protein of Plasmodium gallinaceum. Mol Biochem Parasitol 2000; 105: 61–70.
Gollnick P. Regulation of Bacillus subtilis tip Operon by an RNA-binding protein. Mol Microbiol 1994; 11: 991–997.
Goodwin EB, Okkema PG, Evans TC, Kimble J. Translation al regulation of tra-2 by its 3’ untranslated region controls sexual identity in C. elegans. Cell 1993; 75: 329–339.
Gopal V, Brieba LG, Guajardo R, McAllister WT, Sousa R. Characterization of structural features important for T7 RNAP elongation complex stability reveals competing complex conformations and a role for the non-template strand in RNA displacement. J Mol Biol 1999; 290:411–431.
Görlich D, Mattaj IW. Protein kinesis—nucleocytoplasmic transport. Science 1996; 271: 1513–1518.
Gott JM, Emeson RB. Functions and mechanisms of RNA editing. Annu Rev Genet 2000; 34: 499–531.
Gottlien E. The 3’ untranslated region of localized maternal messages contains a conserved motif involved in mRNA localization. PNAS 1992; 89: 7164–7168.
Gouet P, Diprose JM, Grimes JM, Malby R, Burroughs JN, Zientara S, Stuart DI, Mertens PP. The highly ordered double-stranded RNA genome of bluetongue virus revealed by crystallography. Cell 1999; 97: 481–490.
Graber JH, Cantor CR, Mohr SC, Smith TF. In silico detection of control signals: mRNA 3’-end processing sequences in different species. PNAS 1999; 96: 14055–14060.
Grant CM, Miller PF, Hinnebusch AG. Sequences 5’ of the first upstream open reading frame in GCN4 mRNA are required for efficient translational reinitiation. Nucleic Acids Res 1995; 23: 3980–3988.
Grassi G, Marini JC. Ribozymes: structure, function, and potential therapy for dominant genetic disorders. Ann Med 1996; 28: 499–510.
Graves LE, Segal S, Goodwin EB. TRA-1 regulates the cellular distribution of the tra-2 mRNA in C. elegans. Nature 1999; 399: 802–805.
Gray MW, Covello PS. RNA editing in plant mitochondria and chloroplasts. FASEB J 1993; 7: 64–71.
Gray MW, Hanic-Joyce PJ, Covello PS. Transcription, processing and editing in plant mitochondria. Annu Rev Plant Phys Mol Biol 1992; 43: 145–175.
Gray NK, Hentze MW. Iron regulatory protein prevents binding of the 43S translation pre-initiation complex to ferritin and eALAS mRNAs. EMBO J 1994; 13: 3882–3891.
Gray NK, Costas P, Dandekar T, Ackrell BAC, Hentze MW. Translational regulation of mammalian and Drosophila citric acid cycle enzymes via iron-responsive elements. PNAS 1996; 93: 4925–4930.
Green MR. Biochemical mechanisms of constitutive and regulated pre-mRNA splicing. Annu Rev Cell Biol 1991; 7: 559–599.
Green R, Noller HF. Ribosomes and translation. Annu Rev Biochem 1997; 66: 679–716.
Green PL, Yip MT, Xie Y, Chen IS. Phosphorylation regulates RNA binding by the human T-cell leukemia virus Rex protein. J Virol 1992; 4325–4330.
Greider CW, Blackburn EH. Identification of a specific telomer terminal transferase activity in Tetrahymena extracts. Cell 1985; 43: 405–413.
Greider CW, Blackburn EH. The telomer terminal trasnferase of tetranhymena is a ribonucleoprotein enzyme with two kinds of primer specificity. Cell 1987; 51: 887–898.
Greider CW, Blackburn EH. A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat syntheis. Nature 1989; 337: 331–337.
Grens A, Scheffler IE. The 5’-and 3’-untranslated regions of ornithine-decarboxylase mRNA affect the translational efficiency. J Biol Chem 1990; 265: 11810–11816.
Grillo G, Attimonelli M, Liunni S, Graziano P. CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases. CABIOS 1996; 12: 1–8.
Grishok FJ, Tabara H, Mello CC. Genetic requirements for inheritance of RNAi in C. elegans. Science 2000; 287: 2494–2497.
Grundy FJ, Henkin TM. The rps gene encoding ribosomal protein S4 is autogenously regulated in Bacillus subtilis. J Bacteriol 1991; 173: 4595–4602.
Gu H, Das Gupta J, Schoenberg DR. The poly(A) limiting element is a conserved cis-acting sequence that regulates poly(A) tail length on nuclear pre-mRNA. PNAS 1999; 96: 8943–8948.
Gualberto JM, lamattina L, Bonnard G, Weil JH, Grienenberger JM. RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature 1989; 341: 660–662.
Guan H, Carpenter CD, Simon AE. Requirement of a 5’-proximal linear sequence on minus strand for plus-strand synthesis of a satellite RNA associated with turnip crinkle virus. Virology 2000; 268: 355–362.
Gultyaev AP, van Batenbergh FH, Pleij CW. The computer simulation of RNA folding pathways using a genetic algorithm. J Mol Biol 1995; 250: 37–51.
Gundelfinger ED, Krause E, Melli M, Dobberstein B. The organization of the 7SL RNA in the signal recognition particle. Nucí Acids Res 1983; 11: 7363–7374.
Guo H, Karberg M, Long M, Jones JP 3rd, Sullenger B, Lambowitz AM. Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science 2000; 289: 452–457.
Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD. Three dimensioanl constraints on the higher order structure of RNA: continued development and application of computational sequence analysis methods. Nucleic Acids Res 1992; 20: 5785–5795.
Gutell RR, Cannone JJ, Konings D, Gautheret D. Predicting U-turns in ribosomal RNA with comparative sequence analysis. J Mol Biol 2000; 300: 791–803.
Guthrie C. Messenger RNA splicing in yeast: clues to why the spliceosome is a ribonucleoprotein. Science 1991; 253: 157–163.
Ha I, Wightman B, Ruvkun G. A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation. Genes Dev 1996; 10: 3041–3050.
Hajduk SL, Sabatini RS. Mitochondrial mRNA editing in kinetoplastid protozoa. In: Grosjean H, Benne R (eds) Modification and editing of RNA 1998, 377–393.
Hajduk SL, Harris ME, Pollard VW. RNA editing in kinetoplastid mitochondria. FASEB J 1993; 7: 54–63.
Hake LE, Richter JD. CPEB is a specificity factor that mediates cytoplasmic polyadenylation during Xenopus oocyte maturation. Cell 1994; 79: 617–627.
Hake LE, Méndez R, Richter JD. Specificity of RNA binding by CPEB: requirement for RNA recognition motifs and a novel zink-finger. Mol Cell Biol 1998; 18: 685–693.
Hall BD, Spiegelman S. Sequence complementarity of T2-DNA and T2-specific RNA. PNAS 1964; 47: 137–146.
Hall SL, Padgett RA. Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. J Mol Biol 1994; 239: 357–365.
Hall SL, Padgett RA. Requirement of U12 snRNA for in vivo splicing of a minor class of eukaryotic nuclear pre-mRNA introns. Science 1996; 271: 1716–1718.
Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 1999; 286: 950–952.
Hamilton SE, Simmons CG, Kathiriya IS, Corey DR. Cellular delivery of peptide nucleic acids and inhibition of human telomerase. Chem Biol 1999; 6: 343–351.
Hammond SM, Bernstein E, Beach D, Hannon GJ. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 2000; 404: 293–296.
Han K, Kim HJ. Prediction of common folding structures of homologuos RNAs. Nucleic Acids Res 1993; 21: 1251–1257.
Handa N, Nureki O, Kurimoto K, Kim I, Sakamoto H, Shimura Y, Muto Y, Yokoyama S. Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 1999; 398: 579–585.
Hao Y, Crenshaw T, Moulton T, Newcomb E, Tycko B. Tumour-suppressor activity of H19 RNA. Nature 1993; 365: 764–767.
Harada K, Martin SS, Frankel AD. Selection of RNA-binding peptides in vivo. Nature 1996; 380: 175–179.
Hardin PE, Hall JC, Rosbash M. Feedback of the Drosophila period gene product on circadian cycling of its mRNA levels. Nature 1990; 343: 536–540.
Harley CB, Villeponteau B. Telomeres and telomerases in aging and cancer. Curr Opin Genet Dev 1995; 5: 249–255.
Harley CB, Kim NW. Telomerase and cancer. Important Adv Oncol 1996; 1: 57–67.
Harris ME, Hajduk SL. Kinetoplastid editing: in vitro formation of cytochrome b guide RNA-mRNA chimeras from synthetic substrate RNAs. Cell 1992; 68: 1091–1099.
Hashimoto C, Steitz JA. U4 and U6 RNAs coexist in a single small nuclear ribonucleoprotein particle. Nucleic Acid Res 1984; 12: 3283–3293.
Hemmings-Mieszczak M, Steger G, Hohn T. Alternative structrues of the cauliflower mosaic virus 35S RNA leader: implication for viral expression and replication. J Mol Biol 1997; 267: 1075–1088.
Hendrich BD, Willard HF Epigenetic regulation of gene expression: the effect of altered chromatin structure from yeast to mammals. Hum Mol Genet 1995; 4: 1765–1777.
Henry Y, Wood H, Morrisey JP, Petfalski E, Kearsey S, Tollervey D. The 51 end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J 1994; 13: 2452–2463.
Hentze MW, Kühn LC. Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. PNAS 1996; 93: 8175–8182.
Hentze MW, Kulozik AE. A perfect message: RNA surveillance and nonsense-mediated decay. Cell 1999; 96: 307–310.
Hentze MW, Wright Caughman S, Rouault TA, Barriocanal JG, Dancis A, Harford JB, Klausner RD. Identification of the iron-responsive element for the translational regulation of human ferritin mRNA. Science 1987; 238: 1570–1573.
Herb A, Higuchi M, Sprengel R, Seeburg PH. Q/R site editing in kainate receptor GluR5 and GluR6 pre-mRNAs requires distant intronic sequences. PNAS 93: 1875–1880.
Hermann T, Westhof E. Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA. J Mol Biol 1998; 276: 903–912.
Hertel KJ, Nerschlag D, Uhlenbeck OC. Specificity of hammerhead ribozyme cleavage. EMBO J 1996; 15: 3751–3757.
Herzing LBK, Romer JT, Horn JM, Ash worth A. Xist has properties of the X-chromosome inactivation center. Nature 1997; 386: 272–279.
Hickerson RP, Watkins-Sims CD, Burrows CJ, Atkins JF, Gesteland RF, Felden B. A nickel complex cleaves uridine in folded RNA structures: application to E. coli tmRNA and related engineered molecules. J Mol Biol 1998; 279: 577–87.
Higgins DG, Bleasby AJ, Fuchs R. Comp Appl Biosci 1992; 8: 189–191.
Higgins DG, Thompson JD, Gibson TJ. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 1996; 266: 383–402.
Higgins SJ, Harnes BD (eds). RNA processing—a practical approach. Oxford University Press, 1994.
Higuchi M, Single FN, Köhler M, Sommer B, Sprengel R, Seeburg PH. RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency. Cell 1993; 75: 1361–1370.
Hill KE, Lloyd RS, Burk RF. Conserved nucleotide sequences in the open reading frame and 3’ untranslated region of selenoprotein P mRNA. PNAS 1993; 90: 537–541.
Himeno H, Yoshida S, Soma A, Nishikawa K. Only one nucleotide insertion to the long variable arm confers an efficient serine acceptor activity upon Saccharomyces cerevisiae tRNALeu in vitro. J Mol Biol 1997; 268: 704–711.
Hinkley CS, Blasco MA, Funk WD, Feng J, Villeponteau B, Greider CW, Herr W. The mouse telomerase RNA 5’end lies just upstream of the telomerase template sequence. Nucleic Acids Res 1998; 26: 532–536.
Hinnebusch AG. Translational control of GCN4: gene-specific regulation by phosphorylation of eIF2. In: Hershey J, Mathews M, Sonenberg N (eds) Translational Control. CSHL Press 1996; 199–244.
Hinnebusch AG. Translational reguation of yeast GCN4. A window on factors that control initiator tRNA binding to the ribosome. J Biol Chem 1997; 272: 21661–21664.
Hirsch HH, Nair AP, Backenstoss V, Moroni C. Interleukin-3 mRNA stabilization by a trans-acting mechanosm in autocrine tumors lacking interleukin-3 gene rearrangements. J Biol Chem 1995; 270: 20629–20635.
Ho Y, Waring RB. The maturase encoded by a group I intron from Aspergillus nidulans stabilizes RNA tertiary structure and promotes rapid splicing. J Mol Biol 1999; 292: 987–1001.
Hobbs FW. Palladium-catalyzed synthesis of alkynylamino nucleosides. A universal linker for nucleic acids. J Org Chem 1989; 54: 3420–3422.
Hoch B, Maier RM, Appel K, Igloi GL, Kössel H. Editing of a chloroplast mRNA by creation of an initation codon. Nature 1991; 353: 178–180.
Hockenbery DM. Bcl-2, a novel regulator of cell death. Bioessays 1995; 17: 631–638.
Hodges D, Bernstein SI. Genetic and biochemical analysis of alternative RNA splicing. Academic Press, San Diego, 1994.
Hodges P, Scott J. Apolipoprotein B mRNA editing: a new tier for the control of gene expression. Trends Biochem Sci 1992; 17: 77–81.
Holcik M, Liebhaber SA. Four highly stable eukaryotic mRNAs assemble 3’UTR-protein complexes sharing cis-and trans components. PNAS 1997; 94: 2410–2414.
Holcik M, Korneluk RG. Fuctional characterisation of the X-linked inhibitor of apoptosis (XIAP) internal ribosome entry site element: role of La autoantigen in XIAP translation. Mol Cell Biol 2000; 20: 4648–4657.
Holcik M, Sonenberg N, Korneluk RG. Internal ribosome initiation of translation and the control of cell death. Trends in Genetics 2000; 16: 469–473.
Holley RW, Apgar J, Everett GA. Structure of a ribonucleic acid. Science 1965; 147: 1462–1465.
Honda M, Brown EA, Lemon SM. Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA. RNA 1996; 2: 955–968.
Hornstein E, Harel H, Levy G, Meyuhas O. Overexpression of poly(A)-binding protein down-regulates the translation or the abundance of ist own mRNA. FEBS L 1999; 457: 209–213.
Hotz HR, Lorentz P, Fischer R, Krieger S, Clayton C. Role of 3’UTRs in the regulation of hexose transporter mRNA in T.brucei. Mol Biochem Parasitol 1995; 75: 1–14.
Hoyne PR, Edwards LM, Viari A, Maher LJ 3rd. Searching genomes for sequences with the potential to form intrastrand triple helices. J Mol Biol 2000; 302: 797–809.
Huang H, Liao J, Cohen SN. Poly(A)-and polyíUJ-specific RNA 3’ tail shortening by E. coli ribonuclease E. Nature 1998; 391: 99–102.
Huang J, Villemain J, Padilla R, Sousa R. Mechanisms by which T7 lysozyme specifically regulates T7 RNA polymerase during different phases of transcription. J Mol Biol 1999; 293: 457–475.
Hughes-JM. Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. J Mol Biol 1996; 259: 645–654.
Hughes JMX, Ares MJ. Depletion of U3 small nucleolar RNA inhibits cleavage in the 5’ external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J 1991; 10: 4231–4239.
Huttenhofer A, Boeck A. RNA structures involved in selenoprotein synthesis. In: Simon R, Grunberg-Manago, M. (eds) RNA structure and function. CSHL Press 1998, 603–639.
Huynen M, Gutell R, Konings D. Assessing the reliability of RNA folding using statistical mechanics. J Mol Biol 1997; 267: 1104–1112.
Ikawa Y, Shiraishi H, Inoue T. Minimal catalytic domain of a group I self-splicing intron RNA. Nat Struct Biol 2000; 7: 1032–1035.
International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 2001; 409: 860–922.
Ito K, Uno M, Nakamura Y. A tripeptide’ anticodon’ deciphers stop codons in messenger RNA. Nature 2000; 403: 680–684.
Iverson LE, Mottes JR, Yeager SA, Germeraad SE. Tissue-specific alternative splicing of Shaker potassim channel transcripts result from distinct modes of regulating 3’ splice choice. J Neurobiol 1997; 32: 457–468.
Jackson RJ. Initiation without an end. Nature 1991; 353: 14–15.
Jackson S, Wickens M. Translational controls impiging on the 5’-untranslated region and initiation factor proteins. Curr Opin Gen Dev 1997; 7: 233–241.
Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961; 3: 318–356.
Jacobson A. Poly(A) metabolism and translation: the closed-loop model. In: Hershey J, Mathews M, Sonenberg N (eds) Translational Control. CSHL Press 1996; 451–480.
Jacobson A, Peltz SW. Destabilization of nonsense-containing transcripts in S. cerevisiae. In: Sonenberg N, Hershey JWB, and Mathews MB (eds) Translational Control. CSHL Press 2000; 827–847.
Jacquier A. Self-splicing group II and nuclear pre-mRNA introns: how similar are they? Trends BiochemSci 1990; 15: 351–354.
Jacquier A, Jacquesson-Breuleux N. Splice site selection and the role of the lariat in a group II intron. J Mol Biol 1991; 219: 415–428.
Jan E, Yoon JW, Walterhouse D, Iannoaccone P, Goodwin B. Conservation of the C. elegans tra-2 3’UTR translational control. EMBO J. 1997; 16: 6301–6313.
Jansen R, Tollervey D, Hurt EC. A U3 snoRNP protein with homology to splicing factor PRP4 and Gb domains is required for ribosomal RNA processing. EMBO J 1993; 12: 2549–2558.
Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. Multiple sequence alignment with Clustal X. Trends Biochem Sci. 1998; 23: 403–405.
Jentsch S. When proteins receive deadly messages at birth. Science 1996; 271: 955–956.
Ji Y, Marra A, Rosenberg M, Woodnutt G. Regulated antisense RNA eliminates alpha-toxin virulence in Staphylococcus aureus infection. J Bacteriol 1999; 181: 6585–90.
Jin L, Loyd RV. In situ hybridization: methods and applications. J Clin Lab Anal 1997; 11: 2–9.
Johansson HE, Sproat BS, Melefors O. Reverse transcription using nuclease-resistant primers. Nucleic Acids Res 1993; 21: 2275–2276.
Johnston CM, Nesterova TB, Formstone EJ, Newall AE, Duthie SM, Sheardown SA, Brockdorff N. Developmentally regulated Xist promoter switch mediates initiation of X inactivation. Cell 1998; 94: 809–817.
Jones EM, Gray-Keller M, Art JJ, Fettiplace R. The functional role of alternative splicing of CaC-activated K+ channels in auditory hair cells. Ann NY Acad Sci 1999; 868: 379–385.
Jones JT, Lee SW, Sullenger BA. Tagging ribozymes reaction sites to follow iraní-splicing in mammalian cells. Nature Med 1996; 2: 643–648.
Jung J-E, Karoor V, Sandbaken MG, Lee BJ, Ohama T, Gesteland RF, Atkins JF, Mullenbach GT, Hill KE, Wahba AJ, Hatfield DL. Utilization of selenocysteyl-tRNA 0860 and seryl-tRNA(Ser)Sec in protein synthesis. J Biol Chem 1994; 269: 29739–29745.
Kambach C, Walke S, Young R, Avis JM, de la Fortelle E, Raker VA, Luhrmann R, Li J, Nagai K. Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Ceil 1999; 96: 375–387.
Kan JL, Green MR. Pre-mRNA splicing of IgM exons Ml and M2 is directed by a juxtaposed splicing enhancer and inhibitor. Genes Dev 1999; 13: 462–471.
Kandel-Lewis S, Séraphin B. Role of U6 snRNA in 5’ splice site selection. Science 1993; 262: 2035–2039.
Kang CH, Chan R, Berger I, Lockshin C, Green L, Gold L, Rich A. Crystal structure of the T4 regA translational regulator protein at 1.9 Â resolution. Science 1995; 268: 1170–1173.
Karpen GH, Schaefer JE, Laird CD. A Drosophila rRNA gene located in euchromatin is active in transcription and nucleolus formation. Genes Dev 1988; 2: 1745–1763.
Katsu Y, Yamashita M, Nagahama Y. Translational regulation of cyclin B mRNA by 17alpha,20beta-dihydroxy-4-pregnen-3-one (maturation-inducing hormone) during oocyte maturation I a teleost fish, the goldfish (Carassius auratua). Moll Cell Endocrinol 1999; 158: 79–85.
Kaufman RJ. Double-stranded RNA-activated protein kinase PKR. In: Sonenberg N, Hershey J, Mathews M (eds) Translational Control. CSHL Press 2000: 503–527
Keck JL, Roche DD, Lynch AS, Berger JM. Structure of the RNA polymerase domain of E. coli primase. Science 2000; 287: 2482–2486.
Keenan RJ, Freymann DM, Walter P, Stroud RM. Crystal structure of the signal-sequence binding subunit of the signal recognition particle. Cell 1998; 94: 181–191.
Keller W. No end yet to messenger RNA 3f processing. Cell 1995; 81: 829–832.
Kelley RL, Kuroda MI. Equality for X chromosomes. Science 1995; 270: 1607–1610.
Kenealy MR, Flouriot G, Pope C, Gannon F. The 3’ untranslated region of the human estrogen recpetor gene post-transcriptionally reduces mRNA levels. Biochem Soc Trans 1996; 24: 107.
Kenealy MR, Flouriot G, Sonntag-Buck V, Dandekar T, Brand H, Gannon F. The 3’-untranslated region of the human estrogen receptor alpha gene mediates rapid messenger ribonucleic acid turnover. Endocrinology 2000; 141: 2805–2813.
Ketting RF, Plasterk RH. A genetic link between co-suppression and RNA interference in C. elegance. Nature 2000; 404: 296–298.
Kieft JS and Tinoco I, Jr. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine. Structure 1997; 5. 713–721.
Kiledjian M, Dreyfuss G. Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. EMBO J 1992; 11: 2655–2664.
Kiledjian M, Wang X, Liebhaber SA. Identification of two KH domian proteins in the alpha-globin mRNP stability complex. EMBO J 1995; 14: 43570–4364.
Kim J, Cole JR, Pramanik S. Alignment of possible secondary structures in multiple RNA sequences using simulated annealing. CABIOS 1996; 12: 259–267.
Kim NA, Piatyszek MA, Prowse KR, Harley CB, West MD, Ho PLC, Coviello GM, Wright WE, Weinrich SL, Shay JW. Specific association of human telomerase activity with immortal cells and cancer. Science 1994; 266: 2011–2015.
Kim U, Nishikura K. Double-stranded RNA adenosine deaminase as a potential mammalian RNA editing factor. Semin Cell Biol 1993; 4: 285–293.
Kim-Ha J, Smith JL, Macdonald PM. oskar mRNA is localized to the posterior pole of the Drosophila oocyte. Cell 1991; 66: 23–35.
Kim-Ha J, Webster PJ, Smith JL, Macdonald PM. Multiple RNA regulatory elements mediate distinct steps in the localization of oskar mRNA. Development 1993; 119: 169–178.
Kim-Ha J, Kerr K, Macdonald PM. Translational regulation of oskar mRNA by bruno, an ovarian RNA-binding protein, is essential. Cell 1995; 81: 403–412.
Kiss T, Filipowicz W. Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. Genes Dev 1995; 9: 1411–1424.
Kiss-László Z, Henry Y, Bachellereie J-P, Caizergues-Ferrer M, Kiss T. Site-specific ribose methylation of preribosomal RNA: A novel function for small nucleolar RNAs. Cell 1996; 85: 1077–1088.
Klasens BI, Thiesen M, Virtanen A, Berkhout B. The ability of HIV-1 AAUAAA signal to bind polyadenylation factors is controlled by local RNA structure. Nucleic Acid Res 1999; 27: 446–454.
Klausner RD, Rouault TA, Harford JB. Regulating the fate of mRNA: The role of cellular iron metabolism. Cell 1993; 72: 19–28.
Klootwijk J, Planta RJ. Isolation and characterization of yeast ribosomal RNA precursors and preribosomes. Methods Enzymol 1989; 180: 96–109.
Knight SW, Docherty K. The identification of protein RNA interactions within the 51 UTR of human preproinsulin mRNA. Bioch Soc Trans 1991; 19: 120.
Knoop V, Schuster W, Wissinger B, Brennicke A. Trans splicing integrates an exon of 22 nucleotides into the nad5 mRNA in higher plant mitochondria. EMBO J 1991; 10: 3483–3493
Koch G, Dandekar T. RNA-catalysed nucleotide synthesis. Condensation and commentary. Chemtracts-Biochem Mol Biol 1999; 12: 938–943.
Kochetov AV, Ponomarenko MP, Frolov AS, Kisselev LL, Kolchanov NA. Prediction of eukaryotic mRNA translational properties. Bioinformatics 1999; 15: 704–712.
Köhler SA, Menotti E, Kühn LC. Molecular clonino of mouse gycolate oxidase. High evolutionary conservation and presence of iron-responsive element-like sequence in the mRNA. J Biol Chem 1999; 274: 2401–2407.
Kolakofsky D, Hausmann S. Cotranscriptional paramyxovirus mRNA editing: a contradiction in terms? In: Grosjean H, Benne R (eds) Modification and editing of RNA 1998, 13–420.
Kolk MH, van der Graaf M, Wijmenga SS, Pleij CW, Heus HA, Hilbers CW. NMR structure of a classical pseudoknot: interplay of single-and double-stranded RNA. Science 1998; 280: 434–438.
Komatsu Y, Yamashita S, Kazama N, Nobuoka K, Ohtsuka E. Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor. J Mol Biol 2000; 299: 1231–1243.
Komine Y, Kitabatake M, Yokogawa T, Nishikawa K, Inokuchi H. A t-RNA-like structure is present in lOSa RNA, a small stable RNA from Escherichia coli. PNAS 1994; 91: 9223–9227.
Konarska MM, Grabowski PJ, Padgett RA, Sharo PA. Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors. Nature 1985; 313: 552–557.
Konings DAM, Nash MA, Maizel JV, Arlinghaus RB. Novel GACG-hairpin motif in the 5’untranslated region of type (C) retroviruses related to murine leukemia virus. J Virol 1992; 66:632–640.
Koslowsky DJ, Bhat GJ, Perollaz AL, Feagin JE, Stuart K. The MURF3 gene of T. brucei contains multiple domains of extensive editing and is homologous to a subunit of NADH dehydrogenase. Cell 1990; 62: 901–911.
Kozak M. The scanning model for translation: an update. J Cell Biol 1989; 108: 229–241.
Kozak M. Interpreting cDNA sequences: some insights from studies on translation. Mamm-Genome 1996; 7: 563–574.
Krause M, Hirsch D. A trans-spliced leader sequence on actin mRNA in C. elegans. Cell 1987; 49:753–761.
Kreivi J-P, Lamond AI. RNA splicing: Unexpected spliceosome diversity. Curr Biol 1996; 6: 802–805.
Kruys V, Wathelet M, Poupart, Contreras R, Fiers W, Content J, Huez G. The 3’ untranslated region of the human interferon-ß mRNA has an inhibitory effect on translation. Proc Natl Acad Sci USA 1987; 84: 6030–6034.
Kubota S, Kondo S, Eguchi T, Hattori T, Nakanishi T, Pomerantz RJ, Takigawa M. Identification of an RNA element that confers post-transcriptional repression of connective tissue growth factor/hypertrophic chondrocyte specific 24 (ctfg/hcs24) gene: similarities to retroviral RNA-protein interactions. Oncogene 2000; 19: 4773–4786.
Kuchino Y, Muramatsu T. Nonsense suppression in mammalian cells. Biochimie 1996; 78: 1007–1015.
Kudla J, Igloi GL, Metzlaff M, Hagemann R, Kössel H. RNA editing in tobacco chloroplasts leads to the formation of a translatable psbL mRNA by a C to U substitution within the initiation codon. EMBO J 1992; 11: 1099–1103.
Kudo M, Kitamura-Abe S, Shimbo M, Iida Y. Analysis of 51 splice site sequences in mammalian RNA precursors by a subclass method. Comp Appl Biosci 1992; 8: 367–376.
Kufel J, Kirsebom LA. Residues in Escherichia coli RNAse P RNA important for cleavage site selection and divalent metal ion binding. J Mol Biol 1996; 263: 685–698.
Kundu M, Ansari SA, Chepenik LG, Pomerantz RJ, Khalili K, Rappaport J, Amini S. HIV-1 regulatory protein tat induces RNA binding proteins in central nervous system cells that associate with the viral trans-acting response regulatory motif. J Hum Virol 1999; 2: 72–80.
Kuo MY, Chao M, Taylor J. Initiation of replication of the human hepatitis delta virus genome from cloned DNA: role of delta antigen. J Virol 1989; 63: 1945–1950.
Kuroda MI, Palmer MJ, Lucchesi J C. X-chromosome dosage compensation in Drosophila. SeminDevBiol 1993; 4: 107–116.
Kuwabara PE, Okkema PG, Kimble J. tra-2 encodes a membrane protein and may mediate cell communication in the Caenorhabditis elegans sex determination pathway. Mol Cell Biol 1992; 3: 461–473.
Kwon YK, Hecht NB. Binding of a phosphoprotein to the 3’untranslated region of the mouse protamine 2 mRNA temporally represses its translation. MCB 1993; 13: 6547–6557.
Kyprides NC, Ouzounis CA. Mechanisms of specificity in mRNA degradation:Autoregulation and cognate interactions. J Theor Biol 1993; 163: 373–392.
Laforest MJ, Roewer I, Lang BF. Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG’ stop’ codons recognized as leucine. Nucleic Acids Res 1997; 25: 626–632.
Lai EC, Posakony JW. Regulation of Drosophila neurogenesis by RNA:RNA duplexes? Cell 1998; 93: 1103–1104.
Laing LG, Hall KB. A model of the iron-responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. Biochemistry 1996; 35: 13586–13596.
Laird PW. Transsplicing in trypanosomes—archaism or adaptation? Trends Genet 1989; 5: 204–209.
Lambowitz AM, Caprara MG, Zimmerly S, Perlman PS. Group I and group II ribozymes as RNPs: clues to the past and guides to the future. In: Gesteland RF, Cech TR, and Atkins JF (eds) The RNA world, 2nd edn. 1999; 451–485.
Lamond A (ed.) pre-mRNA processing. Molecular Biology Intelligence Unit, RG Landes, Austin, Texas, 1995.
Lamond AI, Earnshaw WC. Structure and function in the nucleus. Science 1998; 280: 547–553.
Lamond AI, Konarska MM, Grabowski PJ, Sharp P. Spliceosome assembly involves the binding and release of U4 small nuclear ribonucleoprotein. Proc Natl Acad Sci 1988; 85: 411–415.
Landers JE, Cassel SL, George DL. Translational enhancement of mdm2 oncogene expression in human tumor cells containing a stabilized wild-type p53 protein. Cancer Res 1997; 57: 3562–3568.
Lazowska J, Jacq C, Slonimski PP. Sequence of introns and flanking exons in wild-type and box3 mutants of cytochrome b reveals an interlaced splicing protein coded by an intron. Cell 1980: 22, 333–348.
Lee CZ, Lin JH, CHao M, McKnight K, Lai MM. RNA binding activity of hepatitis delta antigen involves two arginine-rich motifs and is required for hepatitis delta virus RNA replication. J Virol 1993; 67: 2221–2227.
Lee JT. Disruption of imprinted X inactivation by parent-of-origin effects at TSIX. Cell 2000; 103:17–27.
Lee JT, Jaenisch R. Long-range cis effects of ectopic X-inactivation centres on a mouse autosome. Nature 1997; 386: 275–279.
Lee JT, Strauss WM, Dausman JA, Jaenisch R. A 450-kb transgene displays properties of the mammalian X-inactivation center. Cell 1996; 86: 83–94.
Lee RC, Feinbaum RL, Ambros V. The C.elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75: 843–854.
Legault P, Li J, Mogridge J, Kay LE, Greenblatt J. NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif. Cell 1998; 93: 289–299.
Leontis NB, Westhof E. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs. J Mol Biol 1998; 283: 571–583.
Lerner MR, Boyle JA, Mount SM, Wolin SL, Steitz JA. Are snRNPs involved in splicing? Nature 1980; 283: 220–224.
Lesoon A, Mehta A, Singh R, Chisolm GM, Driscoll DM. An RNA-binding protein recognizes a mammalian selenocysteine insertion sequence element required for cotranslational incorporation of selenocysteine. Mol Cell Biol 1997; 17: 1977–1985.
Lewin AS, Hauswirth WW. Ribozyme gene therapy: application for molecular medicine. Trends Mol Med 2001; 7: 221–228.
Lewis HA, Musunuru K, Jensen KB, Edo C, Chen H, Darnell RB, Burley SK. Sequence specific RNA binding by a nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Cell 2000; 100: 323–332.
Lewis JD, Tollervey D. Like attracts like: getting RNA processing together in the nucleus. Science 2000; 288: 1385–1389.
Li E, Beard C, Jaenisch R. Role for DNA methylation in genomic imprinting. Nature 1993; 366: 362–365.
Li H, Abelson J. Crystal structure of a dimeric archaeal splicing endonuclease. J Mol Biol 2000; 302:639–648.
Li HV, Zagorski J, Fournier MJ. Depletion of U14 small nuclear RNA (snR128) disrupts production of 18S rRNA in Saccharomyces cerevisiae. Mol Cell Biol 1990; 10: 1145–1152.
Li J, Petryshyn RA. Activation of the double-stranded RNA-dependent eIF-2 alpha kinase by cellular RNA from 3T3-F442A cells. Eur J Biochem 1991; 195: 41–48.
Li S, Wilkinson MF. Nonsense surveillance in lymphocytes? Immunity 1998; 8: 135–141.
Li Z, Brow DA. A spontaneous duplication in U6 spliceosomal RNA uncouples the early and late functions of the ACAGA element in vivo. RNA 1996; 2: 879–894.
Liang H, Jost JP. An estrogen-dependent polysomal protein binds to the 5’UTR of the chicken vitellogenin mRNA. Nucleic Acids Res. 1991; 19: 2289–2994.
Lim J, Thomas T, Cavicchioli R. Low temperature regulated DEAD-box RNA helicase from the Antarctic archaeon, Methanococcoides burtonii. J Mol Biol 2000; 297: 553–67.
Limbach PA, Crain PF, McCloskey JA. Summary: the modified nucleosides of RNA. Nucleic Acids Res 1994; 22: 2183–2196.
Lin FT, MacDougald OA, Diehl AM and Lane MD. A 30-kDa alternative translation product of the CCAAT/enhancer binding protein alpha message: transcriptional activator lacking antimitotic activity. Proc Natl Acad Sci U S A 1993; 90, 9606–9610.
Liphardt J, Napthine S, Kontos H, Brierley I. Evidence for an RNA pseudoknot loop-helix interaction essential for efficient-1 ribosomal frameshifting. J Mol Biol 1999; 288: 321–35.
Lisacek F, Diaz Y, Michel F. J Mol Biol 1994; 235: 1206–1217.
Lohse PA, Szostak JW. Ribozyme-catalyzed amino-aeid transfer reactions. Nature 1996; 381: 442–444.
Lomakin IB, Hellen CU, Pestova TV. Physical association of eukaryotic initiation factor 4G (eIF4G) with eIF4A strongly enhances binding of eIF4G to the internal ribosomal entry site of encephalomyocarditis virus and is required for internal initiation of translation. Mol Cell Biol 2000; 20: 6019–6029.
Lomeli H, Mosbacher J, Melcher T, Höger T, Geiger JRP, Kuner T, Monyer H, Higuchi M, bach A, Seeburg P. Control of kinetic properties of AMPA receptor channels by nuclear RNA editing. Science 1994; 266: 1709–1713.
Lonergan KM, Gray MW. Editing of transfer RNAs in Acanthamoeba castellana mitochondria. Science 1993; 259: 812–816.
Long DM, Uhlenbeck OC. Self-cleaving catalytic RNA. FASEB J 1993; 7: 25–30.
Lowe TM, Eddy SR. A computational screen for methylation guide snoRNAs in yeast. Science 1999; 283: 1168–1171.
Lu XM, Fischman AJ, Jyawook SL, Hendricks K, Tompkins RG, Yarmush ML. Antisense DNA delivery in vivo: liver targeting by receptor-mediated uptake. J Nucí Med 1994; 35: 269–275.
Lund E, Dahlberg JE. Proofreading and aminoacylation of tRNAs before export from the nucleus [see comments]. Science 1998; 282: 2082–2085.
Luo G, Chao M, Hsieh SY, Sureau C, Nishikura K, Taylor J. A specific base transition occurs on replicating hepatitis delta virus RNA. J Virol 1990; 64: 1021–1027.
Luo Y, Kurz J, MacAfee N, Krause MO. C-myc deregulation during transformation induction: involvement of 7SK RNA. J Cell Biochem 1997; 64: 313–327.
Lütcke H. Signal recognition particle (SRP), a ubiquitous initiator of protein translocation. Eur J Biochem 1995 Mar 15; 228(3): 531–535(50).
Lykke-Andersen K. Structural characteristics of the stable RNA introns of archaeal hyperthermophiles and their splicing junctions. J Mol Biol 1994; 243: 846–855.
Lyon MF. Pinpointing the center. Nature 1996; 379: 116–117.
Ma Y, Mathews MB. Comparative analysis of the structure and function of adenovirus virus--associated RNAs. J Virol 1993; 67: 6605–6617.
Macdonald PM, Struhl G. Cw-acting sequences responsible for anterior localization of bicoid mRNA in Drosophila embryos. Nature 1988; 336: 595–59(8).
Macejak DG, Sarnow P. Internal initiation of translation mediated by the 51 leader of a cellular mRNA [see comments]. Nature 1991; 353: 90–94.
Mackie GA. Ribonuclease E is a 5’-end-dependent endonuclease. Nature 1998; 395: 720–723.
Maden BEH. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucleic Acids Res 1990; 39: 241–303.
Madhani HD, Guthrie C. A novel base-pairing interactiuon between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Ceil 1992; 71: 803–817.
Madhani HD, Bordonné R, Guthrie C. Mutliple roles for U6 snRNA in the splicing pathway. Genes Dev 1990; 4: 2264–2277.
Madhani HD, Guthrie C. Dynamic RNA-RNA interactions in the spliceosome. Annu Rev Genet 1994; 28: 1–26.
Mahendran R, Spottswood MS, Ghate A, Ling ML, Jeng K, Miller DL. Editing of the mitochondrial small subunit rRNA in Physarum polycephalum [published erratum appears in EMBO J 1994 Mar 15;13(6):1493]. Embo J 1994; 13, 232–240.
Mahendran R, Spottswood MR, Miller DL. RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature 1991; 349: 434–438.
Maier RM, Hoch B, Zeitz P, Kössel H. Internal editing of the maize chloroplast ndhA transcript restores codons for conserved amino acids. Plant Cell 1992; 4: 609–616.
Malim MH, Bohnlein E, Hauber J, Cullen BR. Functional dissection of the HIV-1 Rev trans-activator-derivation of a irans-dominant repressor of Rev function. Cell 1989; 58: 205–214.
Malyankar UM, Rittling SR, Coumar A, Denhardt DT. The mitogen-regulated protein/proliferin transcript is degraded in primary mouse embryo fibroblasts but not 3T3 nuclei: altered RNA processing correlates with immortalization. Proc Natl Acad Sci USA 1994; 91: 335–339.
Manley JL. A complex protein assembly catalyzes polyadenylation of mRNA precursors. Curr Opin Genet Dev 1995; 5: 222–228.
Manley JL, Proudfoot NJ. RNA 3’ends: Formation and function-meeting review. Genes Dev 1994; 8: 259–264.
Maquat LE. Nonsense-mediated RNA decay in mammalian cells: a splicing-dependent means to down-regulate the levels of mRNAs that prematurely terminate translation. In: Sonenberg N, Hershey JWB, Mathews MB (eds.) Translational control of gene expression 2000: 849–868.
Marcand S, Gilson E, Shore D. A protein-counting mechanism for telomere length regulation in yeast. Science 1997; 275: 986–990.
Marchfelder A, Brennicke A, Binder S. RNA editing is required for efficient excision of tRNA(Phe) from precursors in plant mitochondria. J Biol Chem 1996; 271: 1898–1903.
Markussen FH, Michon AM, Breitwieser W, Ephrussi A. Translational control of oskar generates short OSK, the isoform that induces polar granule assembly. Development 1995; 121:3723–3732.
Marczinke B, Fisher R, Vidakovic M, Bloys AJ, Brierley I. Secondary structure and mutational analysis of the ribosomal frameshift signal of rous sarcoma virus. J Mol Biol 1998; 284: 205–225.
Martin F, Schaller A, Eglite S, Schümperli D, Müller B. The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein. EMBO J 1997; 16: 769–778.
Mascotti DP, Goessling LS, Rup D, Thach RE. Effects of the ferritin open reading frame on translational induction by iron. Prog Nucleic Acids Res Mol Biol 1996; 55: 121–133.
Maxwell ES, Fournier MJ. The small nucleolar RNAs. Annu Rev Biochem 1995; 35: 897–934.
McEachern M, Blackburn EH. A conserved sequence motif within the exceptional telomeric sequence of budding yeast. Proc Natl Acad Sci USA 1994; 91: 3453–3457.
McGarry TJ, Lindquist S. The preferential translation of Drosophila hsp70 mRNA requires sequences in the untranslated leader. Cell 1985; 42: 903–911.
McGrew LL, Dworkin-Rastl E, Dworkin MB, Richter JD. Poly(A) elongation during Xenopus oocyte maturation is required for translational recruitment and is mediated by a short sequence element. Genes Dev 1989; 3: 803–815.
McGuire AM, Hughes JD, Church GM. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res 2000; 10: 744–757.
McKay DB, Wedekind JE. Small ribozymes. In: Gesteland RF, Cech TR, Atkins JF (eds) The RNA world., 2nd edition 1999; 265–286.
McPheeters DS, Abelson J. Mutational analysis of the yeast U2 snRNA suggests a structural similarity to the catalytic core of group I introns. Cell 1992; 71: 819–831.
Mehldau G, Myers G. A system for pattern matching applications on bioComp. Appl Biosci 1993; 9: 299–314.
Melcher T, Maas S, Herb A, Sprengel R, Seeburg PH, Higuchi M. A mammalian RNA editing enzyme. Nature 1996; 379: 460–464.
Meiler VH, Wu KH, Roman G, Kuroda MI, Davis RL. roxi RNA paints the X chromosome of male Drosophila and is regulated by the dosage compensation system. Cell 1997; 88: 445–457.
Melefors Ö. Translational regulation in vivo of the Drosophila melanogaster mRNA encoding succinate dehydrogenase iron protein via iron responsive elements. Biochem Biophys Res Commun 1996; 221: 437–441.
Melefors Ö, Hentze MW. Translational regulation by mRNA/protein interactions in eukaryotic cells: ferritin and beyond. BioEssays 1993; 15: 85–90.
Melefors Ö, Goosen B, Johansson HE, Stripecke R, Gray NK, Hentze MW. Translational control of 5-aminolevulinate synthase mRNA by iron-responsive elements in erythroid cells. J Biol Chem 1993; 268: 5974–5978.
Méndez R, Hake LE, Andresson T, Littlepage LE, Rudermann JV, Richter JD. Phosphorylation of CPE binding factor by Eg2 regulates translation of c-mos mRNA. Nature 2000; 404: 302–307.
Méndez R, Kannenganti GKM, Ryan K, Manley JL, Richter JD. Phosphorylation of CPEB by Eg2 mediates the recruitment of CPSF into an active catoplasmic polyadenylation complex. Mol Cell 2000; 6: 1253–1259.
Merrick WC, Hershey, JWB. The pathway and mechanism of eukaryotic protein synthesis. In Translational Control, J Hershey, M Mathews, N Sonenberg, eds (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press) 1996, 31–69.
Meyuhas O, Hornstein E. Translational control of TOP mRNAs. In: Sonenberg N, Hershey JWB, Mathews MB (eds.) Translational control of gene expression 2000; 671–693.
Meyuhas O, Avni D, Shama S. Translational control of ribosomal protein mRNAs in eukayotes. In: Translational control (Hershey JWB, Mathews MB and Sonenberg N) Cold Spring Harbor 1996: 363–388.
Michael WM, Choi M, Drezfuss G. A nuclear export signal in hnRNP Al: a signal-mediated, temperature-dependent nuclear protein export pathway. Cell 1995; 83: 415–422.
Michael WM, Eder PS, Dreyfuss G.T he K nuclear shuttling domain: a novel signal for nuclear import and nuclear export in hnRNP K protein. EMBO J 1997; 16: 3587–3598.
Michel F, Ferat J-L. Structure and activities of group II introns. Annu Rev Biochem 1995; 64:435–461.
Miller D, Mahendran R, Spottswood M, Costandy H, Wang S, Ling ML, Yang N. Insertional editing in mitochondria of Physarum. Semin Cell Biol 1993; 4: 261–266.
Miller ED, Plante CA, Kim KH, Brown JW, Hemenway C. Stem-loop structure in the 5’ region of potato virus X genome required for plus-strand RNA accumulation. J Mol Biol 1998; 284:591–608.
Mills DR, Kramer FR, Spiegelman S. Complete nucleotide sequence of a replicating RNA molecule. Science 1973; 180: 916–927.
Mills DR, Peterson RL, Spiegelman S. An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc. Natl. Acad. Sci. USA 1967; 58: 271–274.
Milosavljevic A, Jurka J. Discovering simple DNA sequences by the algorithm significance method. Comp Appl Biosci 1993; 9: 407–411.
Miranda G, Schuppli D, Barrera I, Hausherr C, Sogo JM, Weber H. Recognition of bacteriophage Q? plus strand RNA as a template by Q? replicase: role of RNA interactions mediated by ribosomal proteins SI and host factor. J Mol Biol 1997; 267: 1089–1103.
Mirkin CA, Letsinger RL, Mucic RC, Storhoff JJ. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 1996; 382: 581–583.
Misra R, Reeves PR. Role of micF in the tolC-mediated regulation of OmpF, a major outer membrane protein of Escherichia coli K-12. J Bacteriol 1987; 169: 4722–4730.
Mistelli T. Cell biology of transcription and pre-mRNA splicing: nuclear architecture meets nuclear function. J Cell Sci. 2000 Jun;113 ( Pt 11): 1841–1849. Review.
Mitchell JR, Cheng J, Collins K. A box H/ACA small nucleolar RNA-like domain at the human telomerase RNA 3’ end. Mol Cell Biol 1999 Jan; 19:567–576.
Mittermaier A, Varani L, Muhandiram DR, Kay LE, Varani G. Changes in side-chain and backbone dynamics identify determinants of specificity in RNA recognition by human UlA protein. J Mol Biol 1999; 294: 967–979.
Mize GJ, Rúan H, Low JJ, Morris DR. The inhibitory upstream open reading frame from mammalian S-adenosylmethionine decarboxylase mRNA has a strict sequence specificity in critical positions. J Biol Chem 1998; 273, 32500–32505.
Mizuno T, Chou M-Y, Inouye M. A unique mechanism regulating gene expression: Translational inhibtion by a complementary RNA transcript (micRNA). Proc Natl Acad Sci USA 1984; 81: 1966–1970.
Mobarak CD, Anderson KD, Morin M, Beckel-Michener A, Rogers SL, Furneaux H, King P, Perrone-Bizzozero NI. The RNA-binding protein HuD is required for GAP-43 mRNA stability, GAP-43 gene expression, and PKC-dependent neurite outgrowth in PC 12 cells. Mol Biol Cell 2000; 11: 3191–3203.
Moore MJ, Sharp PA. Evidence for two active sites in the spliceosome provided by stereochemistry of pre-mRNA splicing. Nature 1993; 365: 364–368.
Moore MJ, Query CC, Sharp PA. Splicing of precursors to mRNA by the spliceosome. In: The RNA world Gesteland RF, Atkins JF, Plainview, NY: Cold Spring Harbor Lab. Press. 1993: 303–357.
Moras D, Poterszman A. Protein-RNA interactions: Getting into the major groove. Curr Biol 1996; 6: 530–532.
Morris DR, Geballe AP. Upstream open reading frames as regulators of mRNA translation. Mol Cell Biol 2000; 20: 8635–8642.
Morrisey JP, Tollervey D. Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol Cell. Biol 1993; 13: 2469–2477.
Morrisey JP, Tollervey D. Birth of the snoRNPs-the evolution of RNase MRP and the eukaryotic pre-rRNA procesing sytem. Trends Biochem Sci 1995; 20: 78–82.
Moss EG, Lee RC, Ambros V. The cold shock domain proten lin-28 contols developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 1997; 88: 637–646.
Mount SM. AT-AC introns: An ATtACk on dogma. Science 1996; 271: 1690–1692.
Mourrain P, Beclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, Jouette D, Lacombe AM, Nikic S, Picault N, Remoue K, Sanial M, Vo TA, Vaucheret H. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 2000; 101: 533–542.
Mowry KL, Steitz JA. Identification of the human U7snRNP as one of several factors involved in the 3’ end maturation of histone pre-messenger RNAs. Science 1987; 238: 1682–1687.
Moxham CM, Malbon CC. Insulin action impaired by deficiency of the G-protein subunit G¿_2. Nature 1996; 379: 840–844.
Moxham CM, Hod Y, Malbon CC. Induction of G alpha i2-specific antisense RNA in vivo inhibits neonatal growth. Science 1993; 260: 991–995.
Muckenthaler M, Gray NK, Hentze MW. IRP-1 binding to ferritin mRNA prevents the recruitment of the small ribosomal subunit by the cap-binding complex eIF4F. Mol Cell 1998: 2, 383–388.
Mühlrad D, Parker R. Mutations affecting stability and deadenylation of the yeast MFA2 transcript. Genes Dev 1992; 6: 2100–2111.
Müller B, Link J, Smythe C. Assembly of U7 small nuclear ribonucleoprotein particle and histone RNA 3’ processing in Xenopus egg extracts. J Biol Chem 2000; 275: 24284–93.
Müller PP, Hinnebusch AG. Multiple upstream AUG codons mediate translational control of GCN4. Cell 1986; 45: 201–207.
Müllner EW, Kühn LC. A stem-loop in the 3’ untranslated region mediates iron-dependent regulation of transferrin receptor mRNA stability in the cytoplasm. Cell 1988; 53: 815–825.
Murray JB, Terwey DP, Maloney L, Karpeisky A, Usman N, Beigelman L, Scott WG. The structural basis of hammerhaed ribozyme self-cleavage. Cell 1998; 92: 665–673.
Musco G, Stier G, Joseph C, Castiglione-Morelli MA, Nilges M, Gibson TJ, Pastore A. Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. Cell 1996; 85: 237–245.
Nagai K, Mattaj IW. RNA-protein interactions. IRL Press, Oxford, N.Y., 1994.
Nagalla SR, Barry BJ, Spindel ER. Cloning of complementary DNAs encoding the amphibian bombesin-like peptides Phe8 and Leu8 phyllolitorin from Phyllomedusa sauvagei: potential role of U to C RNA editing in generating neuropeptide diversity. Mol Endocrinol 1994; 8: 943–951.
Nakamura TM et al. Telomerase catalytic subunit homologs from fission yeast and human. Science 1997; 277: 955–959.
Nakielny S, Dreyfuss G. Nuclear export of proteins and RNAs. Curr Op Cell Biol 1997; 9: 420–429.
Narayanam R, Akhtar S. Antisense therapy. Curr Opin Oncol 1996; 8: 509–515.
Navaratnam N, Patel D, Shah RR, Greeve JC, Powell LM, Knott TJ, Scott J. An additional editing site is present in apolipoprotein B mRNA. Nucleic Acids Res 1991; 19: 1741–1744.
Nedde DN, Ward MO. Visualizing relationships between nucleic acid sequences using correlation images. Comp Appl Biosci 1993; 9: 331–335.
Nesbitt SM, Erlacher HA, Fedor MJ. The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects. J Mol Biol 1999; 286: 1009–1024.
Neugebauer KM, Roth MB. Distribution of pre-mRNA splicing factors at sites of RNA Polymerasen transcription. Genes Dev 1997; 11: 1148–1159.
Newman A. Small nuclear RNAs and pre-mRNA splicing. Curr Op in Cell Biol 1994; 6: 360–367.
Newmann A, Norman C. U5 snRNAs interacts with exon sequences at 5’ and 3’ splice sites. Cell 1992; 68: 743–754.
Ni J, Tien, A, Fournier M. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 1997; 89: 565–573.
Nichols RC, Wang XW, Tang J, Hamilton BJ, High FA, Herschan HR, Rigby WF. The RGG domain in hnRNP A2 affects subcellular localization. Exp Cell Res 2000; 256: 522–532.
Nicoll M, Akerib CC, Meyer BJ. X-chromosome-counting mechanisms that determine nematode sex. Nature 1997; 388: 200–204.
Nicoloso M, Qu LH, Michot B, Bachellerie J-P. Intron-encoded, antisens small nucleolar RNAs: THe characterization of nine novel species points to their direct role as guides for the 2?-O-ribose methylation of rRNAs. J Mol Biol 260: 178–195.
Nilsen TW. RNA-RNA interactions in the spliceosome: unravelling the ties that bind. Cell 1994a; 78: 1–4.
Nilsen TW. Unusual strategies of gene expression and control in parasites. Science 1994b; 264, 1868–1869.
Nilsen TW. Trans-splicing: an update. Mol Biochem Parasitol 1995; 73: 1–6.
Nilsen TW. A parallel spliceosome. Science 1996; 273: 1813
Novick RP, Ross HF, Projan SJ et al. Synthesis of staphylococcal virulence factors is controlled by a regulatory RNA molecule. EMBO J 1993; 12: 3967–3975.
Nowakowski J, Tinoco I. RNA structure and stability. Semina in Virol; 1997; 8: 153–165.
Nugent JM, Palmer JD. RNA-mediated transfer of the gene coxll from the mitochondrion to the nucleus during flowering plant evolution. Cell 1991; 66: 473–481.
Nyce JW, Metzger WJ. DNA antisense therapy for asthma in an animal model. Nature 1997; 385:721–725.
Ogura H, Agata H, Xie M, Odaka T, Furutani H. A study of learning splice sites of DNA sequence by neural networks. Comput Biol Med 1997; 27: 67–75.
Oh SK, Scott MP, Sarnow P. Homeotic gene Antennapedia mRNA contains 5’-noncoding sequences that confer translational initiation by internal ribosome binding. Genes Dev 1992; 6: 1643–1653.
Ohno M, Ségref A, Bachi A, Wilm M, Mattaj IW. PHAX, a mediator of U snRNA nuclear export whose activity is regulated by phosphorylation. Cell 2000; 101: 187–198.
Oliver AW, Bogdarina I, Schroeder E, Taylor IA, Kneale GG. Preferential binding of fd gene 5 protein to tetraplex nucleic acid structures. J Mol Biol 2000; 301: 575–584.
Olsthoorn RC, Licis N, Van Duin J. Leeway and constraints in the forced evolution of a regulatory RNA helix. EMBO J 1994; 13: 2660–2668.
Olsthoorn RC, Garde G, Dayhuff T, Atkins JF, Van Duin J. Nucleotide sequence of a single stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures. Virology 1995; 206: 611–625.
Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP. Homologs of small nucleolar RNAs in Archaea. Science 2000; 288: 517–22.
Osada Y, Saito R, Tomita M. Analysis of base-pairing potentials between 16S rRNA and 5’ UTR for translation initiation in various prokaryotes. Bioinformatics. 1999 Jul-Aug; 15(7-8):578–581.
Oskouian B, Rangan VS, Smith S. Regulatory elements in the first intron of the rat fatty acid synthase gene. Biochem J 1997; 324: 113–121.
Ossipow V, Descombes P, Schibler U. CCAAT/enhancer-binding protein mRNA is translated into multiple proteins with different transcription activation potentials. Proc Natl Acad Sci USA 1993; 90: 8219–8223.
Ostareck DH, Ostareck-Lederer A, Wilm M, Thiele BJ, Mann M, Hentze MW. mRNA silencing in erytroid differentiation: hnRNP K and hnRNP El regulate 15-lipoxygenase translation from the 3’ end. Cell 1997; 89: 597–606.
Ostareck DH, Ostareck-Lederer A, Shatsky IN, Hentze MW. Lipoxygenase mRNA silencing in erythroid differentiation: The 3’UTR regultaory complex controls 60S ribosomal subunit joining. Cell 2001, in press.
Ostareck-Lederer A, Ostareck DH, Standart N, Thiele BJ. Translation of 15-lipoxygenase mRNA is inhibited by a protein that binds to a repeated sequence in the 31 untranslated region. EMBO J 1994; 13: 1476–1481.
Ostareck-Lederer A, Ostareck DH, Hentze MW. Cytoplasmic regulatory functions of the KH-domain proteins hnRNPs K and E1/E2. Trends Biochem Sci 1998; 23, 409–411.
Pachnis V, Belayew A, Tilghman S. Locus unlinked to „-fetoprotein under the control of the murine raf and Rif genes. Proc Natl Acad Sci USA 1984; 81: 5523–5527.
Paillart J-C, Berthoux L, Ottmann M, Darlix J-L, Marquet R, Ehresmann B, Ehresmann C. A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis. J Virol 1996; 8348–8354.
Palla F, Melfi R, Di Geatano L, Bonura C, Anello L, Alessandro C, Spinelli G. Regulation of the sea urchin early H2A histone gene expression depends on the modulator element and on sequences located near the 3’ end. Biol Chem 1999; 380: 159–165.
Pan T. Novel RNA substrates for the ribozyme from Bacillus subtilis ribonuclease P identified by in vitro selection. Biochemistry 1995; 34: 8458–8464.
Pan T, Dichtl B, Uhlenbeck O. Properties of an in vitro selected Pb++ cleavage motif. Biochemistry 1994; 33: 9561–9565.
Pandey NB, Marzluff WF. The stem-loop structure at the 3’end of histone mRNA is necesary and sufficient for regulation of histone mRNA stability. Mol Cell Biol 1987; 7: 4557–4559.
Parker R, Siliciano PG, Guthrie C. Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. Cell 1987; 49: 229–239.
Parker R, Simmons T, Shuster EO, Siliciano PG, Guthrie C. Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable sextuple mutant. Mol Cell Biol 1988; 8: 3150–3159.
Paul AV, van Boom JH, Filippov D, Wimmer E. Protein-primed RNA synthesis by purified poliovirus RNA polymerase. Nature 1998; 393: 280–284.
Pedersen AG, Baldi P, Chauvin Y, Brunak S. DNA structure in human RNA polymerase II promoters. J Mol Biol 1998; 281: 663–673.
Pelletier J, Kaplan G, Racaniello VR and Sonenberg N. Cap-independent translation of poliovirus mRNA is conferred by sequence elements within the 5’ noncoding region. Mol Cell Biol 1988; 8: 1103–1112.
Pellizzoni L, Lotti F, Rutjes SA, Pierandrei-Amaldi P. Involvement of the Xenopus laevis Ro60 autoantigen in the alternative interaction of La and CNBP proteins with the 5’UTR of L4 ribosomal protein mRNA. J Mol Biol 1998; 281: 593–608.
Peltz SW, Ross J. Autogenous rgulation of histone mRNA decay by histone proteins in a cell-free system. Mol Cell Biol 1987; 7: 536–540.
Peltz SW, Brown AH and Jacobson A. mRNA destabilization triggered by premature translational termination depends on at least three cis-acting sequence elements and one trans-acting factor. Genes Dev 1993; 7, 1737–1754.
Pelle R, Murphy NB. In vivo UV-cross-linking hybridization: a powerful technique for isolating RNA binding proteins. Application to trypanosome mini-exon derived RNA. Nucleic Acids Res 1993; 25: 2453–2458.
Pellizzoni L, Lotti F, Maras B, Pierandrei-Amaldi P. Cellular nucleic acid binding protein binds a conserved region of the 5’UTR of Xenopus laevis ribosomal protein mRNA. 1997; J Mol Biol 1997; 267: 264–275.
Penal va LO, Ruiz MF, Ortega A, Granadino B, Vincente L, Segarra C, Valcarcel J, Sanchez L. The Drosophile fl(2)d gene, required for female-specific splicing of Sxl and tra pre-mRNAs, encodes a novel nuclear protein with HQ-rich domain. Genetics 2000; 155: 129–139.
Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N. Requirement for XIST in X chromosome inactivation. Nature 1996; 379: 131–137
Percudani R, Pavesi A, Ottonello S. Transfer RNA gene redundancy and translational selection in Saccharomyces cereviaise. J.Mol Biol 1997; 268, 322–330.
Perry RP. RNA processing comes of age. J Cell Biol 1981; 91: 28s-38s.
Pesóle G, Liuni S, D’Souza M. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics 2000 May; 16:439–450.
Pestova TV, Hellen CU, Wimmer E. A conserved AUG triplet in the 5’ nontranslated region of poliovirus can function as an initiation codon in vitro and in vivo. Virology 1994; 204: 729–737.
Pestova TV, Hellen CU, Shatsky IN. Canonical eukaryotic initiation factors determine initiation of translation by internal ribosomal entry. Mol Cell Biol 1996; 16: 6859–6869.
Pestova TV, Lomakin IB, Lee JH, Choi SK, Dever TE, and Hellen CU (2000). The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature (403), 332–5.
Pestova TV, Shatsky IN, Fletcher SP, Jackson RJ, Hellen CU. A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev 1998; 12: 67–83.
Pokrywka NJ, Stephenson EC. Microtubules are a general component of mRNA localization systems in Drosophila oocytes. Dev Biol 1995; 167: 363–370.
Poison AG, Bass BL. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J 1994; 13: 5701–5711.
Poison AG, Bass BL, Casey JL. RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase. Nature 1996; 380: 454–456.
Poola I, Koduri S, Châtra S, Clarke R. Identification of twenty alternatively spliced estrogen receptor alpha mRNAs in breast cancer cell lines and tumors using splice targeted primer approach. J Steroid Biochem Mol Biol 2000; 72: 249–58.
Powell LM, Wallis SC, Pease RJ, Edwards YH, Knott TJ, Scott J. A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 1987; 50: 831–840.
Powers T, Noller HF. The 530 loop of 16S rRNA: a signal to EF-Tu? Trends Genet 1994; 10, 27–31.
Preiss T, Hentze MW. Dual function of the messenger RNA cap structure in poly(A)-tail-promoted translation in yeast. Nature 1998; 392: 516–20.
Prescutti C, Ciafr SA, Bozzoni I. The ribosomal protein L2 in Sxerevisiae controls the level of accumulation of its own mRNA. EMBO J 1991; 8: 2215–2221.
Price DH and Gray MW. A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii. Rna 1999; 5, 302–317.
Price DH, Gray MW. Editing of tRNA. In: Grosjean H and Benne R (eds.). Modification and Editing of RNA 1998; 289–305.
Price SR, Evans PR, Nagai K. Crystal structure of the spliceosomal U2B”-U2A’ protein complex bound to a fragment of U2 small nuclear RNA. Nature 1998; 394: 645–650.
Proud CG. p70 S6 kinase: an enigma with variations. Trends Biochem 1996; 23: 181–184.
Puoti A, Kimble J. The hermaphrodite sperm/oocyte switch requires the Caenorhabditis elegans homologs of PRP2 and PRP22. Proc Natl Acad Sci USA 2000; 97: 3276–3281.
Purdey M. The UK epidemic of BSE: slow virus or chronic pestizide initiated modification of the prion protein? Med Hypothesis 1996; 46: 445–454.
Pütz J, Florentz C, Benselet F, Giegé R. A single methyl group prevents the mischarging of a tRNA. Struct Biol 1994; 1: 580–582.
Pyronnet S, Pradayrol L, Sonenberg N. A cell cycle-dependent internal ribosome entry site. Mol Cell 2000; 5, 607–616.
Raghunathan, PL, Guthrie, C. RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2. Curr Biol 1998; 8: 847–855.
Ralle T, Gremmels D, Stick R. Translational control of nuclear lamin Bl mRNA during oogenesis and early development of Xenopus. Mech Dev 1999; 84: 89–101.
Ramchandani S, MacLeod AR, Pinard M, von Hofe E, Szyf M. Inhibition of tumorigenesis by a cytosine-DNA, methyltransferase, antisense oligodeoxynucleotide. Proc Natl Acad Sci USA 1997; 94: 684–689.
Raney A, Baron AC, Mize GJ, Law GL, Morris DR. In vitro translation of the upstream open reading frame in the mammalian mRNA encoding S-adenosylmethionine decarboxylase. J Biol Chem 2000; 275: 24444–24450.
Rastan S. Non-random X-chromosome inactivation in mouse X-autosome translocation embryos: location of the inactivation centre. Embryol Exp Morphol 1983; 78: 1–22.
Rastan S, Brown SDM. The search for the mouse X-chromosome inactivation centre. Genet Res 1990; 56: 99–106.
Ratajczak MZ, Kant JA, Luger SM et al. In vivo treatment of human leukemia in a seid mouse model with c-myb antisense oligodeoxynucleotides. Proc Natl Acad Sci USA 1992; 89:11823–11827.
Reich CI, VanHoy RW, Porter GL, Wise JA. Mutations at the 3’ splice site can be supressed by compensatory base changes in Ul snRNA in fission yeast. Cell 1992; 69: 1159–1169.
Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 2000; 403: 901–906.
Rendahl KG, Jones KR, Kulkarni SJ, Bagully SH, Hall JC. The dissonance at the no-on-transient-A locus of D.melanogaster: genetic control of courtship song and visual behaviors by a protein with putative RNA binding domain. J Neurosci 1992; 12: 390–407.
Ribes V, Römisch K, Giner A, Dobberstein B, Tollervey D. E.coli 4.5S RNA is part of a ribonucleoprotein particle that has properties related to signal recognition particle. Cell 1990; 63:591–600.
Richter JD. Translational control during early development. BioEssays 1991; 13: 179–183.
Richter JD. Cytoplasmic polyadenylation in development and beyond. Microbiol. Mol. Biol. Rev. 1999; 63: 446–456.
Richter JD. Influence of polyadenylation-induced translation on metatoan development and neuronal synaptic function. In: Sonenberg N, Hershey JWB, Mathews MB (eds.) Translational control of gene Expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 1996:785–805.
Rinke J, Appel B, Digweed M, Luhrmann R. Localization of a base-paired interaction between small nuclear RNAs U4 and U6 in intact U4/U6 ribonucleoprotein particles by psoralen cross-linking. J Mol Biol 1985; 185: 721–731.
Rio DC. Splicing of mRNA, modulation, regulation and role in development. Curr Opin Genet Dev 1993; 3: 574–584.
Ripmaster TL, Woolford JL Jr. A protein containing conserved RNA-recognition motifs is associated with the ribosomal subunits in Saccharomyces cerevisiae. Nucleic Acids Res 1993; 21: 3211–3216.
Rizzetto M, Canese MG, Gerin JL, London WT, Sly DL, Purcell RH. Transmission of the hepatitis B virus-associated delta antigen to chimpanzees. J Infect Dis 1980a; 141: 590–602
Rizzetto M, Hoyer B, Canese MG, Shih JWK, Purcell RH, Gerin JL. delta Agent: association of delta antigen with hepatitis B surface antigen and RNA in serum of delta-infected chimpanzees. Proc Natl Acad Sci USA 1980b; 77: 6124–6128.
Robbins J, Dilworth SM, Laskey RA, Dingwall C. Two interdependent basic domains in nucleoplasm nuclear targeting sequence: identification of a class of bipartite nuclear targeting sequences. Cell 1991; 64: 615–623.
Rogers J, Wall R. A mechanism for RNA splicing. Proc Natl Acad Sci USA 1980; 77: 1877–1879.
Rother M, Wiking R, Commans S, Bock A. Indentification and characterisation of the selenocysteine-specific translation factor SelB from the archaeon Methanococcus jannaschii. J Mol Biol 2000; 299: 351–358.
Rouault TA, Hentze MW, Dancis A, Caughman W, Harford JB, Klausner RD. Influence of altered transcription on the translational control of human ferritin expression. Proc Natl Acad Sci USA 1987; 84: 6335–6339.
Rouault TA, Hentze MW, Haile DJ et al. The iron-responsive element binding protein: A method for the affinity purification of a regulatory RNA-binding protein. Proc Natl Acad Sci USA 1989; 86: 5768–5772.
Rueter SM, Burns CM, Coode SA, Mookherjee P; Emeson RB. Glutamate receptor RNA editing in vitro by enzymatic conversion of adenosine to inosine. Science 1995; 267: 1491–1494.
Rueter SM, Dawson TR, Emeson RB. Regulation of alternative splicing by RNA editing. Nature 1999; 399: 75–80.
Ruiz-Echevarria MJ, Peltz SW. The RNA binding protein Publ modulates the stability of transcripts containing upstream open reading frames. Cell 2000; 101: 741–751.
Ruskin B, Krainer AR, Maniatis T, Green MR. Excision of an intact intron as a novel lariat structure during pre-mRNA splicing in vitro. Cell 1984; 38: 317–331.
Ruvkun G, Giusto J. The Caenorhabditis elegans heterochronic gene lin-14 encodes a nuclear protein that forms a temporal developmental switch. Nature 1989; 338: 313–319.
Ruvolo V, Altszuler R, Levitt A. The transcript encoding the circumsporozoite antigen of Plasmodium berghei utilizes heterogeneous polyadenylation sites. Mol Biochem Parasitol 1993; 57: 137–150.
Ryder SP, Strobel SA. Nucleotide analog interference mapping of the hairpin ribozyme: implications for secondary and tertiary structure formation. J Mol Biol 1999; 291: 295–311.
Rymond BC, Rosbash M. Yeast pre-mRNA splicing. Volume II. The molecular and cellular biology of the yeast Saccharomyces: gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor 1992:143–163.
Sachs A. Physical and functional interactions between the mRNA cap structure and the poly(A) tail. In: Sonenberg N, Hershey JWB, Mathews MB (eds) Translational control of gene expression. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 2000:447–465.
Sachs AB, Kornberg RD. Nuclear polyadenylate binding protein. Mol Cell Biol 1985; 5: 1993–1996.
Sachs AB, Sarnow P, Matthias MW. Starting at the beginning, middle, and end: Translation initiation in eukaryotes. Cell 1997; 89: 831–838.
Saenger W. Principles of nucleic acid structure. Springer Berlin Heidelberg New York 1984.
Saks ME, Sampson JR, Abelson J. Evolution of a transfer RNA gene through a point mutation in the anticodon. Science 1998; 279: 1665–1670.
Saldanha R, Mohr G, Belfort M, Lambowitz AM. Group I and group II introns. FASEB J 1993; 7:15–24.
Sanchez L, Granadino B, Torres M. Sex determination in Drosophila melanogaster: X-linked genes involved in the initial step of sex-lethal activation. Dev Genet 1994; 15: 251–264.
Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D. The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 1999; 97:371–81.
Sarver N, Cairns S. Ribozyme trans-splicing and RNA tagging: Following the messenger. Nat Med 1996; 2: 641–642.
Sasaki H, Jones PA, Chaillet JR, Ferguson-Smith AC, Barton S, Reik W, Surani A. Parental imprinting: potentially active chromatin of the repressed maternal allele of the mouse insulinlike growth factor II (Igf2) gene. Genes Dev 1992; 6: 1843–1856.
Scarabino D, Tocchini-Valentini GP. Influence of substrate structure on cleavage by hammerhead ribozyme. FEBS Lett. 1996; 383: 185–90.
Scherly D, Boelens W, Dathan NA, van Venrooij WJ, Mattaj IW. Major determinants of the specificity of interaction between small nuclear ribonucloeproteins Ul A and U2B” and their cognate RNAs. Nature 1990; 345: 502–506.
Schmidt-Zachmann MS, Nig EA. Protein localization to the nucleolus: A search for targeting domains in nucleolin. J Cell Sci 1993; 799–806.
Schmitt ME. Molecular modeling of the three-dimensional architecture of the RNA component of yeast RNase MRP. J Mol Biol 1999; 292: 827–836.
Schultes EA, Bartel DP. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 2000; 289: 448–452.
Schuppli D, Miranda G, Qiu S, Weber H. A branched stem-loop structure in the M-site of bacteriophage Qbeta RNA is important for template recognition by Qbeta replicase holoenzyme. J Mol Biol 1998; 283: 585–593.
Schuster P, Stadler PF, Renner A. RNA structure and folding: from conventional to new issues in structure prediction. Curr Opin Struct Biol 1997; 7: 229–235.
Schuster W, Brennicke A. Plastid, nuclear and reverse transcriptase sequences in the mitochondrial genome of Oenothera: is genetic information transferred between organelles via RNA? EMBO J 1987; 6: 2857–2863.
Schuster W, Hiesel R, Brennicke A. RNA editing in plant mitochondria. Semin Cell Biol 1993; 4: 279–284.
Schwartz DC, Parker R. mRNA decapping in yeast requires dissociation of the cap binding protein, eukaryotic translation initiation factor 4E. Mol Cell Biol 2000; 20: 7933–7942.
Scott J. A place in the world for RNA editing. Cell 1995; 81: 833–836.
Scott J. Messenger RNA editing and modification. Curr Opin Cell Biol 1989; 1: 1141–1147.
Searls DB. Doing sequence analysis with your printer. Comp Appl Biosci 1993; 9: 421–426.
Ségref A, Sharma K, Doye V, Hellwig A, Huber J, Lührmann R, Hurt E. Mex67p, a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. EMBO J 1997; 16:3256–3271.
SenGupta DJ, Zhang B, Kraemer B, Pochart P, Fields S, Wickens M. A three-hybrid system to detect RNA-protein interactions in vivo. Proc Natl Acad Sci USA 1996; 93: 8496–8501.
Serano TL, Cohen RS. A small predicted stem-loop structure mediates oocyte localization of Drosophila KIO mRNA. Development 1995; 121: 3809–3818.
Séraphin B. How many intronic RNAs? Trends Biochem Sci 1993; 18: 330–331.
Service RF. New probes open windows on gene expression, and more. Science 1998; 280: 1010–1011.
Seto AG, Zaug AJ, Sobel SG, Wolin SL, Cech TR. Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle. Nature 1999; 401: 177–280.
Shah SA, Brunger AT. The 1.8 A crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure. J Mol Biol 1999; 285: 1577–1588.
Sharma PM, Bowman M, Madden SL, Rauscher FJ 3rd, Sukumar S. RNA editing in the Wilms1 tumor susceptibility gene, WTl. Genes Dev 1994; 8: 720–731.
Sharp PA. Trans splicing: variations on a familiar theme? Cell 1987; 50: 147–148.
Sharp PA. RNAi and double-strand RNA. Genes Dev. 1999; 13: 139–141.
Shatkin AJ. Capping of eukaryotic mRNAs Cell 1976; 9: 645–653.
Shaw G, Kamen R. A conserved AU sequence from the 3’untranslated region of GM-CSF mRNA mediates selective mRNA degradation. Cell 1986; 46: 659–667.
Shen Q, Chu FF, Newburger PE. Sequences in the 3’untranslated region of the human cellular glutathione peroxidase gene are necessary and sufficient for selenocysteine incorporation at the UGA Codon. J Biol Chem 1993; 268: 11463–11469.
Shiman R, Draper DE. Stabilization of RNA tertiary structure by monovalent cations. J Mol Biol 2000; 302: 79–91.
Shimizu A. Molecular mechanisms for immunoglobulin class switching and IgE production. Nippon Rinsho 1996; 54: 440–445.
Short S, Tian D, Short ML, Jungmann RA. Structural determinants for posttranscriptional stabilization of lactate dehydrogenase A mRNA by the protein kinase C signal pathway. J Biol Chem 2000; 275: 12963–9.
Shyu AB, Greenber ME, Belasco JG. The c-fos transcript is targeted for rapid decay by two distinct mRNA degradation pathways. Genes Dev 1989; 3: 60–72.
Shyu AB, Belasco J, Greenberg ME. Two distinct destabilizing elements in the c-fos message trigger deadenylation as a first step in rapid mRNA decay. Genes Dev 1991; 5: 221–231.
Sibbald PR, Sommerfeld H, Argos P. Overseer: a nucleotide sequence searching tool. Comp Appl Biosci 1992; 8: 45–48.
Siegel V, Walter P. Removal of the Alu structural domain from signal recognation particle leaves its protein translocation activity intact. Nature. 1986; 320: 81–84.
Sierakowska H, Sambade MJ, Agrawal S, Kole R. Repair of thalassemic human ?-globin mRNA in mammalian cells by antisense oligonucleotides. Proc Natl Acad Sci USA 1996; 93:12840–12844.
Simard MJ, Chabot B. Control of hnRNP Al alternative splicing: an intron element represses use of the common 3’splice site. Mol Cell Biol 2000; 20: 7353–7562.
Simons RW, Kleckner N. Translational control of IS 10 transposition. Cell 1983; 34: 683–691.
Simons M, Edelman ER, DeKeyser JL, Langer R, Rosenberg RD. Antisense c-myb oligonucleotides inhibit intimai arterial smooth muscle cell accumulation in vivo. Nature 1992; 359: 67–70.
Simpson L. RNA editing-An evolutionary perspective. In: Gesteland RF, Cech TR, Atkins JF (eds.) The RNA World 2nd edn 1999:585–608.
Simpson L, Shaw J. RNA editing and the mitochondrial cryptogenes of kinetoplastid protozoa. Cell 1989; 57: 355–366.
Simpson L, Thiemann OH. Sense from nonsense: RNA editing in mitochondria of kinetoplastid protozoa and slime molds. Cell 1995; 81: 837–840.
Singer MS, Gottschling DE. TLCl: template RNA component of Saccharomyces cerevisiae telomerase. Science 1994; 266: 404–409.
Siomi H, Dreyfuss G. RNA-binding proteins as regulators of gene expression. Curr Opin Genet Dev 1997; 7: 345–353.
Sit TL, Vaewhongs AA, Lommel SA. RNA-mediated trans-activation of transcription from a viral RNA. Science 1998; 281: 829–832.
Skuse GR, Cappione AJ, Sowden M, Metheny LJ and Smith HC. The neurofibromatosis type I messenger RNA undergoes base-modification RNA editing. Nucleic Acids Res 1996; 24, 478–485.
Smith HC. Apolipoprotein B mRNA editing: the sequence to the event. Semin Cell Biol 1993; 4: 267–278
Smith S, de Lange T. TRFl, a mammalian telomeric protein. Trends Genet 1997; 13: 21–26.
Solovyev VV, Lawrence CB. Identifiaction of human gene functional regions based on oligonucleotide composition. Ismb 1993; 1: 371–379.
Soma A, Kumagai, Nishikawa K, Himeno H. The anticodon loop is a major determinant of Saccharomyces cerevisiae tRNA. J Mol Biol 1996; 263: 707–714.
Sontheimer EJ, Steitz JA. The U5 and U6 small nuclear RNAs as active site components of the spliceosome. Science 1993; 262: 1989–1996.
Srivastava SP, Davies MV, Kaufman RJ. Calcium depletion from the endoplasmic reticulum activates the double-stranded RNA-dependent protein kinase(PKR) to inhibit protein synthesis. J Biol Chem 1995; 270: 16619–16624.
Staden R. methods for discovering novel motifs in nucleic acid sequences. Comp Appl Biosci 1989; 5: 293–298.
Staden R. The Staden sequence analysis package. Mol Biotechnol 1996; 5: 233–241.
Staden R, Beal KF, Bonfield JK. The Staden package. Methods Mol Biol 2000; 132: 115–130.
Stams T, Niranjanakumari S, Fierke CA, Christianson DW. Ribonuclease P protein structure: evolutionary origins in the translational apparatus. Science 1998; 280: 752–755.
Stebbins-Boaz B, Richter JD. Translational control during early development. Crit Rev Eukaryot Gene Expr 1997; 7: 73–94.
Stebbins-Boaz B, Cao Q, de Moor CH, Méndez R, Richter JD. Maskin is a CPEB-associated factor that transiently interacts with eIF4E. Mol Cell 1999; 4: 1017–1027.
Steinhauser S, Beckert S, Capesius I, Malek O, Knoop V. Plant mitochondrial RNA editing. J Mol Evol 1999; 48: 303–312.
Steinmann-Zwicky M. Sex deteermination of the Drosophila germ line: tra and dsx control somatic inductive signals. Development 1994; 120: 707–716.
Steitz JA. Splicing takes a holliday. Science 1992; 257: 888–889.
Stöger R, Kubicka P, Liu CG, Kafri T, Razin A, Cedar H, Barlow DP. Maternal-specific methylation of the imprinted mouse Igf2r locus identifies the expressed locus as carrying the imprinting signal. Cell 1993; 73: 61–71.
Stuart K. The RNA editing process in trypanosoma brucei. Semin Cell Biol 1993; 4: 251–260.
Stuart K. RNA editing in mitochondrial mRNA of trypanosomatids. Trends Biochem Sci 1991; 16: 68–72.
Stuart K, Allen TE, Heidmann S, Sciwert SD. RNA editing in kinetoplastid protozoa. Microbiol Mol Biol Rev 1997; 61, 105–120.
Sturm NR, Simpson L. Kinetoplastid DNA minicircles encode guide RNAs for the editing of cytochrome oxidase subunit III mRNA. Cell 1990; 61: 879–884.
Sudarsanakumar C, Xiong Y, Sundaralingam M. Crystal structure of an adenine bulge in the RNA chain of a DNA.RNA hybrid, d(CTCCTCTTC).r(gaagagagag). J Mol Biol 2000; 299:103–12.
Sullenger BA, Cech TR. Tethering ribozymes to a retroviral packaging signal for destruction of viral RNA. Science 1993; 262: 1566–1569.
Sullenger BA, Cech TR. Ribozyme-mediated repair of defective mRNA by targed trans-splicing. Nature 1994; 371: 619–622.
Surdej P, Riedl A, Jacobs-Lorena M. Regulation of mRNA stability in development. Annu Rev Genet. 1994; 28: 263–282.
Sutcliffe JS, Nakao M, Christian S, Orstavik KH, Tommerup N, Ledbetter DH, Beaudet AL. Deletions of a differentially methylated CpG island at the SNRPN gene define a putative imprinting control region. Nat Genet 1994; 8: 52–58.
Swanson MS, Dreyfuss G. Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities. Mol Cell Biol 1988; 8: 2237–2241.
Symons RH. Small catalytic RNAs. Annu Rev Biochem 1992; 61: 641–671.
Tabara H, Sarkissian M, Kelly WG, Fleenor J, Grishok A, Timmons L, Fire A, Mello CC. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 1999; 99: 123–132.
Tarn W-Y, Steitz JA. A novel spliceosome containing U11, U12 and U5 snRNPs excises a monor class (AT-AC) intron in vitro. Cell 1996a; 84: 801–811.
Tarn W-Y, Steitz JA. Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns. Science 1996b; 273: 1824–1832.
Tarun SZ, Jr. and Sachs AB. A common function for mRNA 5’ and 3’ ends in translation initiation in yeast. Genes Dev 1995; 9: 2997–3007.
Tarun SZ, Jr., Sachs AB. Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G. Embo J 1996; 15, 7168–7177.
Tarun SZ, Jr., Wells SE, Deardorff JA and Sachs AB. 1997 Translation initiation factor eIF4G mediates in vitro poly(A) tail-dependent translation. Proc Natl Acad Sci USA 1997; 94: 9046–9051.
Tay J, Hodgman R, Richer JD. The control of cyclin B1 mRNA translation during mouse oocyte maturation. Dev Biol 2000; 221: 1–9.
Teerink H, Voorma HO, Thomas AA. The human insulin-like growth factor II leader 1 contains an internal ribosomal entry site. Biochim Biophys Acta 1995; 1264; 403–408.
Temin HM. RNA-directed DNA synthesis. Sci Am 1972; 226: 24–31.
Thanaraj TA, Argos P. Protein secondary structural types are differentially coded on messenger RNA. Protein Sci 1996; 5: 1973–1983.
Tharun S, He W, Mayes AE, Lennertz P, Beggs JD, Parker R. Yeast Sm-like proteins function in mRNA decapping and decay. Nature 2000; 404: 515–518.
Theimer CA, Wang Y, Hoffman DW, Krisch HM, Giedroc DP. Non-nearest neighbor effects on the thermodynamics of unfolding of a model mRNA pseudoknot. J Mol Biol 1998; 279: 545–564.
Theodorakis NG, Cleveland DW. Translationally coupled degradation of mRNA in eukaryotes. In: Hershey J, Mathews M, Sonenberg N (eds) Translational control Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 1996:631–652.
Theurkauf WE, Hazelrigg TI. In vivo analyses of cytoplasmic transport and cytoskeletal organization during Drosophila oogenesis: characterization of a multi-step anterior localization pathway. Development 1998; 125: 3655–3666.
Thomas JD, Conrad RC, Blumenthal T. The C.elegans trans-spliced leader RNA is bound to Sm and has a trimethylguanosine cap. Cell 1988; 54: 533–539.
Tiwari S, Ramachandran S, Bhattacharya A, Bhattacharya S, Ramaswamy R. Predication of probable genes by Fourier analysis of genomic sequences. CABIOS 1997; 13: 263–270.
Tollervey D, Kiss T. Function and synthesis of small nucleolar RNAs. Curr Opin Biol 1997; 9:337–342.
Tollervey D, Lehtonen H, Carmo-Fonseca M, Hurt EC. The small nucleolar RNP protein NOPl (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J 1991; 10: 573–583.
Tomita K, Ueda T and Watanabe K. RNA editing in the acceptor stem of squid mitochondrial tRNA(Tyr). Nucleic Acids Res 1996, 24, 4987–4991.
Tomita N, Morishita R, Higaki J et al. Transient decrease in high blood pressure by in vivo transfer of antisense oligodeoxynucleotides against rat angiotensinogen. Hypertension 1995; 26:131–136.
Tormay P, Sawers A, Böck A. Role of stoichometry between mRNA, translation factor SelB and selenocysteyl-tRNA in selenoprotein synthesis. Mol Microbiol 1996; 21: 1253–1259.
Touriol C, Morillon A, Gensac MC, Prats H, Prats AC. Expression of human fibroblast growth factor 2 mRNA is post-transcriptionally controlled by a unique destabilizing element present in the 3’-untranslated region between alternative polyadenylation sites. J Biol Chem. 1999; 274,21402–8.
Trifonov EN. Interfering contexts of regulatory sequence elements. CABIOS 1996; 12: 423–429.
Trono D, Feinberg M.B, Baltimore D. HIV-1 Gag mutants can dominantly interfere with the replication of the wild-type virus. Cell 1989; 59: 113–120. CHECK citation spelling
Tuck MT. The formation of internal 6-methyladenine residues in eukaryotic messenger RNA. Int J Biochem 1992; 24: 379–386.
Turk C. Using the SELEX combinatorial chemistry process to find high affinity nucleic acid ligands to target molecules. Methods Mol Biol 1997; 67: 219–230.
Tycowski KT, Smith CM, Shu M-D, Steitz JA. A small nucleolar RNA required for site-specific ribose methylation of rRNA in Xenopus. Proc Natl Acad Sci USA 1996; 93: 14480–14485.
Tzfati Y, Fulton TB, Roy J, Blackburn EH. Template boundary in a yeast telomerase specified by RNA structure. Science 2000; 288: 863–867.
Udem SA, Warner JR. Ribosomal RNA synthesis in Saccharomyces cerevisiae. J Biol Chem 1972; 248: 1412–1416.
Unrau PJ, Bartel DP. RNA-catalysed nucleotide synthesis. Nature 1998; 395: 260–263.
Vagner S, Gensac MC, Maret A, Bayard F, Amalric F, Prats H and Prats AC. Alternative translation of human fibroblast growth factor 2 mRNA occurs by internal entry of ribosomes. Mol Cell Biol 1995; 15: 35–44.
Van Biesen T, Soderbom F, Wagner EG, Frost LS. Structural and functional analyses of the FinP antisense rerulatory system of the F conjugative plasmid. Mol Microbiol 1993; 10: 35–43.
Vanchiere JA, Bellini WJ, Moyer SA. Hypermutation of the phosphoprotein and altered mRNA editing in the hamster neurotrophic strain of measles virus. Virology 1995; 207: 555–561.
Vanet A, Marsan L, Labigne A, Sagot MF. Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma family of promoter signals. J Mol Biol 2000; 297:335–53.
Van Horn DJ, Eisenberg D, O’Brien CA, Wolin SL. Caenorhabditis elegans embryos contain only one major species of Ro RNP. RNA 1995; 1: 293–303.
Van Steensel B, de Lange T. Control of telomere length by the human telomeric protein TRFl. Nature 1997; 385: 740–743.
Varani L, Spillanti MG, Goedert M, Varani G. Structural basis for recognition of the RNA major groove in the tau exon 10 splicing regulatory element by aminoglycoside antibiotics. Nucleic Acids Res 2000; 28: 710–709.
Veldman GM, Brand RC, Klootwijk J, Planta RJ. Some characteristics of processing sites in ribosomal precursor RNA of yeast. Nucl Acid Res 1980; 8: 2907–2920.
Vellard M, Sureau J, Soret C, Martinerie C, Perbol B. A potential splicing factor is encoded by the opposite strand of the trans-spliced c-myb exon. Proc Natl Acad Sci 1992; 89: 2511–2515.
Venema J, Tollervey D. Processing of pre-ribosomal RNA in Saccharomyces cerevisiae. Yeast 1995; 11: 1629–1650.
Venema J, Tollervey D. Ribosome synthesis in Saccharomyces cerevisiae. Annu Rev Genet 1999; 33: 261–311.
Venema J, Henry Y, Tollervey D. Two distinct recognition signals define the site of endonucleolytic cleavage at the 5’ end of yeast 18S rRNA. EMBO J 1995; 14 4883–4892.
Veyrune JL, Campbell GP, Wiseman J, Blachard JM, Hesketh JE. A localisation signal in the 3’ untranslated region of c-myc mRNA targets c-myc mRNA and beta-globin reporter sequences to the perinuclear cytoplasm and cytoskeletal-bound polysomes. J Cell Sci 1996; 109:1185–1194.
Villsen ID, Vester B, Douthwaite S. ErmE methyltransferase recognizes features of the primary and secondary structure in a motif within domain V of 23 S rRNA. J Mol Biol 1999; 286: 365–374.
von Hippel PH, Kowalczykowski SC, Lonberg N, Newport JW, Paul LS, Stormo GD, Gold L. Autoregulation of gene expression. Quantitative evaluation of the expression and function of the bacteriophage T4 gene 32 protein system. J Mol Biol 1982; 162: 795–818.
Wagner EGH, Simons RW. Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol 1994; 48: 713–742.
Walter NG, Yang N, Burke JM. Probing non-selective cation binding in the hairpin ribozyme with Tb(III). J Mol Biol 2000; 298: 539–55.
Warnecke JM, Furtse JP, Hardt WD, Erdmann VA, Hartmann RK. Ribonuclease P (RNaseP) RNA is converted to a Cd++-ribozyme by a single Rp-phosphorothioate modification in the precursor tRNA at the RNAse P cleavage site. Proc Natl Acad Sci USA 1996; 93: 8924–8928.
Wassarmann DA, Steitz JA. Interactions of small nuclear RNAs with precursor messenger RNA during in vitro splicing. Science 1992; 257: 1918–1925.
Wasserman WW, Palumbo M, Thompson W, Fickett JW, Lawrence CE. Human-mouse genome comparisons to locate regulatory sites. Nat Genet 2000; 26: 225–228.
Watson JD. Involvement of RNA in the synthesis of proteins. Science 1963; 140: 17–26.
Wei J, Theil EC. Identification and characterization of the iron regulatory element in the ferritin gene of a plant (soybean). J Biol Chem 2000; 275: 17488–17493.
Wei P, Garber ME, Fang SM, Fischer WH, Jones KA. A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 1998; 92: 451–462.
Weiss G, Houston T, Kastner S, Johrer K, Grunewald K, Brock JH. Regulation of cellular iron metabolism by erythropoietin: activation of iron-regulatory protein and upregulation of transferrin receptor expressin in erythroid cells. Blood 1997; 89: 680–687.
Wells SE, Hillner PE, Vale RD, Sachs AB. Circularization of mRNA by eukaryotic translation initiation factors. Mol Cell 1998; 2, 135–140.
Werner M, Feller A, Messenguy F, Piérard A. The leader peptide of yeast gene CPAl is essential for the translational repression of its expression. Cell 1987; 49: 805–813.
Werstuck G, Green MR. Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998; 282: 296–298.
Wevrick A, Kerns JA, Francke U. Identification of a novel paternally expressed gene in the Prader-Willi syndrome region. Hum Mol Genet 1994; 3: 1877–1882.
Wharton RP, Struhl G. RNA regulatory elements mediate control of Drosophila body pattern by the posterior morphogen nanos. Cell 1991; 67: 955–967.
Wickens M. In the beginnning is the end: regulation of poly(A) addition and removal during early development. TIBS 1990; 15: 320–323 (check end page).
Wickens M, Anderson P, Jackson RJ. Life and death in the cytoplasm: messages from the 3’end. Curr Opin Genet Dev 1997; 7: 220–232.
Wickens M, Goodwin EB; Kimble J, Strickland S, Hentze MW. Translational control of developmental decisions. In: Sonenberg N, Hershey JWB, Mathews MB (eds) Translational control of gene expression Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 2000:295–370.
Wickens M, Takayama K. Deviants-or emissaries. Nature 1994; 367: 17–18.
Wightmann B, Ha I, Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993; 75: 855–862.
Wightman B, Burglin TR, Gatto J, Arasu P, Ruvkun G. Negative regulatory sequences in the lin 14 3’-untranslated regions are necessary to generate a temporal switch during Caenorhabditis elegans development. Genes Dev 1991; 5: 1813–1824.
Will CL, Schneider C, Reed R, Luhrmann R. Identification of both shared and distinct proteins in the major and minor spliceosomes. Science 1999; 284: 2003–2005.
Willard HF, Salz HK. Remodelling chromatin with RNA. Nature 1997; 386: 228–229.
Williams DJ, Hall KB. Experimental and computational studies of the G[UUCG]C RNA tetraloop. J Mol Biol 2000; 297: 1045–1061.
Williams KP, Ciafre S, Tocchini-Valentini GP. Selection of novel Mg++ dependent self cleaving ribozymes. EMBO J. 1995; 14, 4551–4557.
Wilson JE, Pestova TV, Hellen CU, Sarnow P. Initiation of protein synthesis from the A site of the ribosome. Cell 2000a; 102:511–520.
Wilson JE, Powell MJ, Hoover SE and Sarnow P. Naturally occurring dicistronic cricket paralysis virus RNA is regulated by two internal ribosome entry sites. Mol Cell Biol 2000b; 20:4990–4999.
Wilson KS, Conant CR, von Hippel PH. Determinants of the stability of transcription elongation complexes: interactions of the nascent RNA with the DNA template and the RNA polymerase. J Mol Biol 1999; 289: 1179–1194.
Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kaiman S, McCullough MJ, McCusker JH, Stevens DA, Wodicka L, Lockhart DJ, Davis RW. Direct allelic variation scanning of the yeast genome. Science 1998; 281: 1194–1197.
Wissinger B, Schuster W, Brennicke A. Trans splicing in Oenothera mitochondria: nadl mRNAs are edited in exon and trans-splicing group II intron sequences. Cell 1991; 65: 473–482.
Wittop-Koning TH, Schümperli D. RNAs and ribonucleoproteins in recognition and catalysis. Eur J Biochem. 1994; 219: 25–42.
Wolfertstetter F, Freeh K, Herrmann G, Werner T. Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search. CABIO 1997; 12: 71–80.
Wu Q, Krainer AR. Ul-mediated exon definition interactions between AT-AC and GT-AG introns. Science 1996; 274: 1005–1008.
Wu S, Romfo CM, Nilsen TW, Green MR. Functional recognition of the 3’ splice site AG by the splicing factor U2AF35. Nature 1999; 402: 832–835.
Wu TH, Liao SM, McLure WR, Susskind MM. Control of gene expression in bacteriophage P22 by a small antisense RNA. II Characterization of mutatnts defectice in repression. Genes Dev. 1987; 1: 204–212.
Yamanaka K, Minato N, Iwai K. Stabilization of iron regulatory protein 2, IRP2, by aluminium. FEBS Lett 1999; 462: 216–220.
Yamanaka S, Poksay KS, Arnold KS, Innerarity TL. A novel repressor mRNA is edited extensively in livers containing tumors caused by the transgene expression of the apoB mRNA-editing enzyme. Genes Dev 1997; 11: 321–333.
Yanofsky C, Konan KV, Sorsero JB. Some novel transcription attenuation mechanisms usd by bacteria. Biochimie 1996; 78: 1017–1024.
Yarnell WS, Roberts JW. Mechanism of intrinsic transcription termination and antitermination. Science 1999; 284: 611–615.
Ye X, Fong P, Iizuka N, Choate D and Cavener DR. Ultrabithorax and Antennapedia 5’ untranslated regions promote developmentally regulated internal translation initiation. Mol Cell Biol 1997; 17, 1714–1721.
Yean SL, Lin RJ. U4 small nuclear RNA disassociates from a yeast spliceosome and does not participate in the subsequent splicing reaction. Mol Cell Biol 1991; 11: 5571–5577.
Yokobori SI, Paabo S. tRNA editing in metazoans. Nature 1995; 377: 490.
Yong TJ, Gan YY, Toh BH, Sentry JW. Human CKIalpha(I) and CKIalpha S) are encoded by both 2.4-and 4.2.-kb transcripts, the longer containing multiple RNA-destabilizing elements. Biochim Biophys Acta 2000; 1492: 425–433.
Young LS, Dunstan HM, Witte PR, Smith TP, Ottonello S, Spragu KU. A class II transcription factor composed of RNA. Science 1991; 252: 542–546.
Yu Y-T, Steitz JA. Site-specific crosslinking of mammalian Ul 1 and U6atac to the 5’ splice site of an AT-AC intron. Proc Natl Acad Sci USA 1997; 94: 6030–6035.
Yu Y-T, Scharl EC, Smith CM, and Steitz JA The growing world of small nuclear ribonucleoproteins. In: Gesteland RF, Cech TR, and Atkins JF (eds) The RNA World, 2nd edn 1999:487–524.
Zachar Z, Chou TB, Bingham PM. Evidence that a regulatory gene autoregulats splicing of its own transcript. EMBO J 1987; 6: 4105–4111.
Zacharias M, Sklenar H. Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model. J Mol Biol 1999; 289: 261–275.
Zakian VA. Telomers: beginning to understand the end. Science 1995; 270: 1601–1607.
Zahringer J, Baliga BS, Munro HN. Proc Natl Acad Sci USA 1976; 73: 857–861.
Zamore PD, Tuschl T, Sharp PA, Bartel DP. RNAi: double stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 2000; 101: 25–33.
Zavanelli MI, Ares M. Efficient association of U2 snRNPs with pre-mRNA requires an essential U2 RNA structural element. Genes Dev 1991; 5: 2521–2533.
Zeffman A, Hassard S, Varani G, Lever A. The major HIV-1 packaging signal is an extended bulged loop whose structure is altered on interaction with the Gag polyprotein. J Mol Biol 2000; 297: 877–893.
Zhang M, Pierce RA, Wachi H, Mecham RP, Parks WC. An open reading frame element mediates posttranscriptional regulation of tropoelastin and responsivness to transforming growth factor betal. Mol Cell Biol 1999; 19: 7314–7326.
Zheng H, Fu TB, Lazinski D, Taylor J. Editing on the genomic RNA of human hepatitis delta virus. J Virol 1992; 66: 4693–4697.
Zimmerly S, Moran JV, Perlman PS, Lambowitz AM. Group II intron reverse transcriptase in yeast mitochondria. Stabilization and regulation of reverse transcriptase activity by the intron RNA. J Mol Biol 1999; 289: 473–490.
Zorio DA, Blumenthal T. Both subunits of U2AF recognize the 3’ splice site in Caenorhabditis elegans. Nature 1999; 402: 835–838.
Zuker M. On finding all suboptimal foldings of an RNA molecule. Science 1989; 244: 48–52.
Zuker M, Mathews DH, Turner DH. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide in RNA biochemistry and biotechnology. NATO ASI Series, Kluwer, Dordrecht, 1999: 11–43.
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Dandekar, T. (2002). References. In: Dandekar, T. (eds) RNA Motifs and Regulatory Elements. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56298-3_9
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