Skip to main content
SpringerLink
Log in

Long Noncoding RNAs in Mammalian Development and Diseases

  • Chapter
  • First Online:
Long Non Coding RNA Biology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1008))

Abstract

Following analysis of sequenced genomes and transcriptome of many eukaryotes, it is evident that virtually all protein-coding genes have already been discovered. These advances have highlighted an intriguing paradox whereby the relative amount of protein-coding sequences remain constant but nonprotein-coding sequences increase consistently in parallel to increasing evolutionary complexity. It is established that differences between species map to nonprotein-coding regions of the genome that surprisingly is transcribed extensively. These transcripts regulate epigenetic processes and constitute an important layer of regulatory information essential for organismal development and play a causative role in diseases. The noncoding RNA-directed regulatory circuit controls complex characteristics. Sequence variations in noncoding RNAs influence evolution, quantitative traits, and disease susceptibility. This chapter presents an account on a class of such noncoding transcripts that are longer than 200 nucleotides (long noncoding RNA—lncRNA) in mammalian development and diseases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F et al (2012) Landscape of transcription in human cells. Nature 489(7414):101–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145–166

    Article  CAS  PubMed  Google Scholar 

  3. Wilusz JE, JnBaptiste CK, LY L, Kuhn CD, Joshua-Tor L, Sharp PA (2012) A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 26(21):2392–2407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Peschansky VJ, Wahlestedt C (2014) Non-coding RNAs as direct and indirect modulators of epigenetic regulation. Epigenetics 9(1):3–12

    Article  CAS  PubMed  Google Scholar 

  5. Mattick JS, Rinn JL (2015) Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol 22(1):5–7

    Article  CAS  PubMed  Google Scholar 

  6. Guil S, Esteller M (2012) Cis-acting noncoding RNAs: friends and foes. Nat Struct Mol Biol 19(11):1068–1075

    Article  CAS  PubMed  Google Scholar 

  7. Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23(13):1494–1504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775–1789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Batista PJ, Chang HY (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell 152(6):1298–1307

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Wapinski O, Chang HY (2011) Long noncoding RNAs and human disease. Trends Cell Biol 21(6):354–361

    Article  CAS  PubMed  Google Scholar 

  11. Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, Chen Y, Liu XS (2013) Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol 20(7):908–913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915–1927

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP, Ulitsky I (2015) Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Rep 11(7):1110–1122

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Diederichs S (2014) The four dimensions of noncoding RNA conservation. Trends Genet 30(4):121–123

    Article  CAS  PubMed  Google Scholar 

  15. Mortimer SA, Kidwell MA, Doudna JA (2014) Insights into RNA structure and function from genome-wide studies. Nat Rev Genet 15(7):469–479

    Article  CAS  PubMed  Google Scholar 

  16. Mattick JS, Taft RJ, Faulkner GJ (2010) A global view of genomic information--moving beyond the gene and the master regulator. Trends Genet 26(1):21–28

    Article  CAS  PubMed  Google Scholar 

  17. Surani MA, Barton SC, Norris ML (1984) Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308(5959):548–550

    Article  CAS  Google Scholar 

  18. McGrath J, Solter D (1984) Inability of mouse blastomere nuclei transferred to enucleated zygotes to support development in vitro. Science 226(4680):1317–1319

    Article  CAS  PubMed  Google Scholar 

  19. Kelsey G, Feil R (2013) New insights into establishment and maintenance of DNA methylation imprints in mammals. Philos Trans R Soc Lond Ser B Biol Sci 368(1609):20110336

    Article  CAS  Google Scholar 

  20. Wan LB, Bartolomei MS (2008) Regulation of imprinting in clusters: noncoding RNAs versus insulators. Adv Genet 61:207–223

    CAS  PubMed  Google Scholar 

  21. Kota SK, Feil R (2010) Epigenetic transitions in germ cell development and meiosis. Dev Cell 19(5):675–686

    Article  CAS  PubMed  Google Scholar 

  22. Smallwood SA, Kelsey G (2012) De novo DNA methylation: a germ cell perspective. Trends Genet 28(1):33–42

    Article  CAS  PubMed  Google Scholar 

  23. Bartolomei MS, Zemel S, Tilghman SM (1991) Parental imprinting of the mouse H19 gene. Nature 351(6322):153–155

    Article  CAS  PubMed  Google Scholar 

  24. Zhang Y, Tycko B (1992) Monoallelic expression of the human H19 gene. Nat Genet 1(1):40–44

    Article  CAS  PubMed  Google Scholar 

  25. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32(2):232–246

    Article  CAS  PubMed  Google Scholar 

  26. Sleutels F, Zwart R, Barlow DP (2002) The non-coding air RNA is required for silencing autosomal imprinted genes. Nature 415(6873):810–813

    Article  CAS  PubMed  Google Scholar 

  27. de los Santos T, Schweizer J, Rees CA, Francke U (2000) Small evolutionarily conserved RNA, resembling C/D box small nucleolar RNA, is transcribed from PWCR1, a novel imprinted gene in the Prader-Willi deletion region, which is highly expressed in brain. Am J Hum Genet 67(5):1067–1082

    Article  PubMed  PubMed Central  Google Scholar 

  28. Wevrick R, Francke U (1997) An imprinted mouse transcript homologous to the human imprinted in Prader-Willi syndrome (IPW) gene. Hum Mol Genet 6(2):325–332

    Article  CAS  PubMed  Google Scholar 

  29. Chamberlain SJ, Brannan CI (2001) The Prader-Willi syndrome imprinting center activates the paternally expressed murine Ube3a antisense transcript but represses paternal Ube3a. Genomics 73(3):316–322

    Article  CAS  PubMed  Google Scholar 

  30. Seitz H, Youngson N, Lin SP, Dalbert S, Paulsen M, Bachellerie JP, Ferguson-Smith AC, Cavaille J (2003) Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat Genet 34(3):261–262

    Article  CAS  PubMed  Google Scholar 

  31. Hatada I, Morita S, Obata Y, Sotomaru Y, Shimoda M, Kono T (2001) Identification of a new imprinted gene, Rian, on mouse chromosome 12 by fluorescent differential display screening. J Biochem 130(2):187–190

    Article  CAS  PubMed  Google Scholar 

  32. Lin SP, Youngson N, Takada S, Seitz H, Reik W, Paulsen M, Cavaille J, Ferguson-Smith AC (2003) Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse chromosome 12. Nat Genet 35(1):97–102

    Article  CAS  PubMed  Google Scholar 

  33. Liu J, Yu S, Litman D, Chen W, Weinstein LS (2000) Identification of a methylation imprint mark within the mouse Gnas locus. Mol Cell Biol 20(16):5808–5817

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Williamson CM, Ball ST, Dawson C, Mehta S, Beechey CV, Fray M, Teboul L, Dear TN, Kelsey G, Peters J (2011) Uncoupling antisense-mediated silencing and DNA methylation in the imprinted Gnas cluster. PLoS Genet 7(3):e1001347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Poirier F, Chan CT, Timmons PM, Robertson EJ, Evans MJ, Rigby PW (1991) The murine H19 gene is activated during embryonic stem cell differentiation in vitro and at the time of implantation in the developing embryo. Development 113(4):1105–1114

    CAS  PubMed  Google Scholar 

  36. Kurukuti S, Tiwari VK, Tavoosidana G, Pugacheva E, Murrell A, Zhao Z, Lobanenkov V, Reik W, Ohlsson R (2006) CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2. Proc Natl Acad Sci U S A 103(28):10684–10689

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Lewis A, Murrell A (2004) Genomic imprinting: CTCF protects the boundaries. Curr Biol 14(7):R284–R286

    Article  CAS  PubMed  Google Scholar 

  38. Gabory A, Ripoche MA, Le Digarcher A, Watrin F, Ziyyat A, Forne T, Jammes H, Ainscough JF, Surani MA, Journot L et al (2009) H19 acts as a trans regulator of the imprinted gene network controlling growth in mice. Development 136(20):3413–3421

    Article  CAS  PubMed  Google Scholar 

  39. Monnier P, Martinet C, Pontis J, Stancheva I, Ait-Si-Ali S, Dandolo L (2013) H19 lncRNA controls gene expression of the imprinted gene network by recruiting MBD1. Proc Natl Acad Sci U S A 110(51):20693–20698

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Kallen AN, Zhou XB, Xu J, Qiao C, Ma J, Yan L, Lu L, Liu C, Yi JS, Zhang H et al (2013) The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell 52(1):101–112

    Article  CAS  PubMed  Google Scholar 

  41. Dey BK, Pfeifer K, Dutta A (2014) The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration. Genes Dev 28(5):491–501

    Article  PubMed  PubMed Central  Google Scholar 

  42. Giovarelli M, Bucci G, Ramos A, Bordo D, Wilusz CJ, Chen CY, Puppo M, Briata P, Gherzi R (2014) H19 long noncoding RNA controls the mRNA decay promoting function of KSRP. Proc Natl Acad Sci U S A 111(47):E5023–E5028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Kanduri C (2016) Long noncoding RNAs: lessons from genomic imprinting. Biochim Biophys Acta 1859(1):102–111

    Article  CAS  PubMed  Google Scholar 

  44. Redrup L, Branco MR, Perdeaux ER, Krueger C, Lewis A, Santos F, Nagano T, Cobb BS, Fraser P, Reik W (2009) The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 136(4):525–530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Smilinich NJ, Day CD, Fitzpatrick GV, Caldwell GM, Lossie AC, Cooper PR, Smallwood AC, Joyce JA, Schofield PN, Reik W et al (1999) A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome. Proc Natl Acad Sci U S A 96(14):8064–8069

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Mohammad F, Mondal T, Guseva N, Pandey GK, Kanduri C (2010) Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 137(15):2493–2499

    Article  CAS  PubMed  Google Scholar 

  47. Fitzpatrick GV, Soloway PD, Higgins MJ (2002) Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat Genet 32(3):426–431

    Article  CAS  PubMed  Google Scholar 

  48. Mancini-Dinardo D, Steele SJ, Levorse JM, Ingram RS, Tilghman SM (2006) Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev 20(10):1268–1282

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Mohammad F, Pandey GK, Mondal T, Enroth S, Redrup L, Gyllensten U, Kanduri C (2012) Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing. Development 139(15):2792–2803

    Article  CAS  PubMed  Google Scholar 

  50. Terranova R, Yokobayashi S, Stadler MB, Otte AP, van Lohuizen M, Orkin SH, Peters AH (2008) Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell 15(5):668–679

    Article  CAS  PubMed  Google Scholar 

  51. Umlauf D, Goto Y, Cao R, Cerqueira F, Wagschal A, Zhang Y, Feil R (2004) Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nat Genet 36(12):1296–1300

    Article  CAS  PubMed  Google Scholar 

  52. Barr ML, Bertram EG (1949) A morphological distinction between neurones of the male and female, and the behaviour of the nucleolar satellite during accelerated nucleoprotein synthesis. Nature 163(4148):676

    Article  CAS  PubMed  Google Scholar 

  53. Ohno S, Kaplan WD, Kinosita R (1959) Formation of the sex chromatin by a single X-chromosome in liver cells of Rattus norvegicus. Exp Cell Res 18:415–418

    Article  CAS  PubMed  Google Scholar 

  54. Lyon MF (1961) Gene action in the X-chromosome of the mouse (Mus musculus L). Nature 190:372–373

    Article  CAS  PubMed  Google Scholar 

  55. Borsani G, Tonlorenzi R, Simmler MC, Dandolo L, Arnaud D, Capra V, Grompe M, Pizzuti A, Muzny D, Lawrence C et al (1991) Characterization of a murine gene expressed from the inactive X chromosome. Nature 351(6324):325–329

    Article  CAS  PubMed  Google Scholar 

  56. Lee JT, Lu N (1999) Targeted mutagenesis of Tsix leads to nonrandom X inactivation. Cell 99(1):47–57

    Article  CAS  PubMed  Google Scholar 

  57. Kay GF, Barton SC, Surani MA, Rastan S (1994) Imprinting and X chromosome counting mechanisms determine Xist expression in early mouse development. Cell 77(5):639–650

    Article  CAS  PubMed  Google Scholar 

  58. Clerc P, Avner P (1998) Role of the region 3′ to Xist exon 6 in the counting process of X-chromosome inactivation. Nat Genet 19(3):249–253

    Article  CAS  PubMed  Google Scholar 

  59. Lee JT (2005) Regulation of X-chromosome counting by Tsix and Xite sequences. Science 309(5735):768–771

    Article  CAS  PubMed  Google Scholar 

  60. Bacher CP, Guggiari M, Brors B, Augui S, Clerc P, Avner P, Eils R, Heard E (2006) Transient colocalization of X-inactivation centres accompanies the initiation of X inactivation. Nat Cell Biol 8(3):293–299

    Article  CAS  PubMed  Google Scholar 

  61. Xu N, Tsai CL, Lee JT (2006) Transient homologous chromosome pairing marks the onset of X inactivation. Science 311(5764):1149–1152

    Article  CAS  PubMed  Google Scholar 

  62. Xu N, Donohoe ME, Silva SS, Lee JT (2007) Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat Genet 39(11):1390–1396

    Article  CAS  PubMed  Google Scholar 

  63. Donohoe ME, Silva SS, Pinter SF, Xu N, Lee JT (2009) The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature 460(7251):128–132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Sun BK, Deaton AM, Lee JT (2006) A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol Cell 21(5):617–628

    Article  CAS  PubMed  Google Scholar 

  65. Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT (2008) Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 322(5902):750–756

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Penny GD, Kay GF, Sheardown SA, Rastan S, Brockdorff N (1996) Requirement for Xist in X chromosome inactivation. Nature 379(6561):131–137

    Article  CAS  PubMed  Google Scholar 

  67. Morey C, Navarro P, Debrand E, Avner P, Rougeulle C, Clerc P (2004) The region 3′ to Xist mediates X chromosome counting and H3 Lys-4 dimethylation within the Xist gene. EMBO J 23(3):594–604

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Ogawa Y, Lee JT (2003) Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Mol Cell 11(3):731–743

    Article  CAS  PubMed  Google Scholar 

  69. Cohen DE, Davidow LS, Erwin JA, Xu N, Warshawsky D, Lee JT (2007) The DXPas34 repeat regulates random and imprinted X inactivation. Dev Cell 12(1):57–71

    Article  CAS  PubMed  Google Scholar 

  70. Anguera MC, Ma W, Clift D, Namekawa S, Kelleher RJ III, Lee JT (2011) Tsx produces a long noncoding RNA and has general functions in the germline, stem cells, and brain. PLoS Genet 7(9):e1002248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, Piolot T, van Berkum NL, Meisig J, Sedat J et al (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485(7398):381–385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Tian D, Sun S, Lee JT (2010) The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143(3):390–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Sun S, Del Rosario BC, Szanto A, Ogawa Y, Jeon Y, Lee JT (2013) Jpx RNA activates Xist by evicting CTCF. Cell 153(7):1537–1551

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C (2011) Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum Mol Genet 20(4):705–718

    Article  CAS  PubMed  Google Scholar 

  75. McGinnis W, Krumlauf R (1992) Homeobox genes and axial patterning. Cell 68(2):283–302

    Article  CAS  PubMed  Google Scholar 

  76. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235):223–227

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Maamar H, Cabili MN, Rinn J, Raj A (2013) Linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes Dev 27(11):1260–1271

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Yin Y, Yan P, Lu J, Song G, Zhu Y, Li Z, Zhao Y, Shen B, Huang X, Zhu H et al (2015) Opposing roles for the lncRNA haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation. Cell Stem Cell 16(5):504–516

    Article  CAS  PubMed  Google Scholar 

  79. Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR, Kapranov P, Weissman SM, Newburger PE (2009) A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood 113(11):2526–2534

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Zhang X, Weissman SM, Newburger PE (2014) Long intergenic non-coding RNA HOTAIRM1 regulates cell cycle progression during myeloid maturation in NB4 human promyelocytic leukemia cells. RNA Biol 11(6):777–787

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Zhao H, Zhang X, Frazao JB, Condino-Neto A, Newburger PE (2013) HOX antisense lincRNA HOXA-AS2 is an apoptosis repressor in all trans retinoic acid treated NB4 promyelocytic leukemia cells. J Cell Biochem 114(10):2375–2383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Hsieh-Li HM, Witte DP, Weinstein M, Branford W, Li H, Small K, Potter SS (1995) Hoxa 11 structure, extensive antisense transcription, and function in male and female fertility. Development 121(5):1373–1385

    CAS  PubMed  Google Scholar 

  83. Sasaki YT, Sano M, Kin T, Asai K, Hirose T (2007) Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus. Biochem Biophys Res Commun 357(3):724–730

    Article  CAS  PubMed  Google Scholar 

  84. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA et al (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472(7341):120–124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Ahn Y, Mullan HE, Krumlauf R (2014) Long-range regulation by shared retinoic acid response elements modulates dynamic expression of posterior Hoxb genes in CNS development. Dev Biol 388(1):134–144

    Article  CAS  PubMed  Google Scholar 

  86. De Kumar B, Parrish ME, Slaughter BD, Unruh JR, Gogol M, Seidel C, Paulson A, Li H, Gaudenz K, Peak A et al (2015) Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Res 25(8):1229–1243

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  87. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7):1311–1323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329(5992):689–693

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Schorderet P, Duboule D (2011) Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet 7(5):e1002071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Delpretti S, Montavon T, Leleu M, Joye E, Tzika A, Milinkovitch M, Duboule D (2013) Multiple enhancers regulate Hoxd genes and the Hotdog LncRNA during cecum budding. Cell Rep 5(1):137–150

    Article  CAS  PubMed  Google Scholar 

  91. Yarmishyn AA, Batagov AO, Tan JZ, Sundaram GM, Sampath P, Kuznetsov VA, Kurochkin IV (2014) HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome. BMC Genomics 15(Suppl 9):S7

    Article  PubMed  PubMed Central  Google Scholar 

  92. Kaneko S, Li G, Son J, CF X, Margueron R, Neubert TA, Reinberg D (2010) Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev 24(23):2615–2620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Li L, Liu B, Wapinski OL, Tsai MC, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA et al (2013) Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep 5(1):3–12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Ge XS, Ma HJ, Zheng XH, Ruan HL, Liao XY, Xue WQ, Chen YB, Zhang Y, Jia WH (2013) HOTAIR, a prognostic factor in esophageal squamous cell carcinoma, inhibits WIF-1 expression and activates Wnt pathway. Cancer Sci 104(12):1675–1682

    Article  CAS  PubMed  Google Scholar 

  95. Battistelli C, Cicchini C, Santangelo L, Tramontano A, Grassi L, Gonzalez FJ, de Nonno V, Grassi G, Amicone L, Tripodi M (2016) The snail repressor recruits EZH2 to specific genomic sites through the enrollment of the lncRNA HOTAIR in epithelial-to-mesenchymal transition. Oncogene 36(7):942–955

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  96. Berrondo C, Flax J, Kucherov V, Siebert A, Osinski T, Rosenberg A, Fucile C, Richheimer S, Beckham CJ (2016) Expression of the long non-coding RNA HOTAIR correlates with disease progression in bladder cancer and is contained in bladder cancer patient urinary exosomes. PLoS One 11(1):e0147236

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  97. Lee M, Kim HJ, Kim SW, Park SA, Chun KH, Cho NH, Song YS, Kim YT (2016) The long non-coding RNA HOTAIR increases tumour growth and invasion in cervical cancer by targeting the notch pathway. Oncotarget 7(28):44558–44571

    Article  PubMed  PubMed Central  Google Scholar 

  98. Luo ZF, Zhao D, Li XQ, Cui YX, Ma N, CX L, Liu MY, Zhou Y (2016) Clinical significance of HOTAIR expression in colon cancer. World J Gastroenterol 22(22):5254–5259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Milevskiy MJ, Al-Ejeh F, Saunus JM, Northwood KS, Bailey PJ, Betts JA, McCart Reed AE, Nephew KP, Stone A, Gee JM et al (2016) Long-range regulators of the lncRNA HOTAIR enhance its prognostic potential in breast cancer. Hum Mol Genet 25(15):3269–3283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Heubach J, Monsior J, Deenen R, Niegisch G, Szarvas T, Niedworok C, Schulz WA, Hoffmann MJ (2015) The long noncoding RNA HOTAIR has tissue and cell type-dependent effects on HOX gene expression and phenotype of urothelial cancer cells. Mol Cancer 14:108

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Zheng P, Xiong Q, Wu Y, Chen Y, Chen Z, Fleming J, Gao D, Bi L, Ge F (2015) Quantitative proteomics analysis reveals novel insights into mechanisms of action of long noncoding RNA Hox transcript antisense intergenic RNA (HOTAIR) in HeLa cells. Mol Cell Proteomics 14(6):1447–1463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Flynn RA, Chang HY (2014) Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell 14(6):752–761

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE et al (2012) Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev 26(4):338–343

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J et al (2013) Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493(7431):231–235

    Article  CAS  PubMed  Google Scholar 

  105. Han P, Li W, Lin CH, Yang J, Shang C, Nurnberg ST, Jin KK, Xu W, Lin CY, Lin CJ et al (2014) A long noncoding RNA protects the heart from pathological hypertrophy. Nature 514(7520):102–106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M et al (2013) Multiple knockout mouse models reveal lincRNAs are required for life and brain development. eLife 2:e01749

    Article  PubMed  PubMed Central  Google Scholar 

  107. Atianand MK, Hu W, Satpathy AT, Shen Y, Ricci EP, Alvarez-Dominguez JR, Bhatta A, Schattgen SA, McGowan JD, Blin J et al (2016) A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation. Cell 165(7):1672–1685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Alvarez-Dominguez JR, Hu W, Yuan B, Shi J, Park SS, Gromatzky AA, van Oudenaarden A, Lodish HF (2014) Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood 123(4):570–581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Klein U, Lia M, Crespo M, Siegel R, Shen Q, Mo T, Ambesi-Impiombato A, Califano A, Migliazza A, Bhagat G et al (2010) The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell 17(1):28–40

    Article  CAS  PubMed  Google Scholar 

  110. Young TL, Matsuda T, Cepko CL (2005) The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr Biol 15(6):501–512

    Article  CAS  PubMed  Google Scholar 

  111. Rapicavoli NA, Poth EM, Blackshaw S (2010) The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol 10:49

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  112. Rapicavoli NA, Poth EM, Zhu H, Blackshaw S (2011) The long noncoding RNA Six3OS acts in trans to regulate retinal development by modulating Six3 activity. Neural Dev 6:32

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Krol J, Krol I, Alvarez CP, Fiscella M, Hierlemann A, Roska B, Filipowicz W (2015) A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architecture. Nat Commun 6:7305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Meola N, Pizzo M, Alfano G, Surace EM, Banfi S (2012) The long noncoding RNA Vax2os1 controls the cell cycle progression of photoreceptor progenitors in the mouse retina. RNA 18(1):111–123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Vausort M, Wagner DR, Devaux Y (2014) Long noncoding RNAs in patients with acute myocardial infarction. Circ Res 115(7):668–677

    Article  CAS  PubMed  Google Scholar 

  116. Korostowski L, Sedlak N, Engel N (2012) The Kcnq1ot1 long non-coding RNA affects chromatin conformation and expression of Kcnq1, but does not regulate its imprinting in the developing heart. PLoS Genet 8(9):e1002956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Yap KL, Li S, Munoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 38(5):662–674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Holdt LM, Beutner F, Scholz M, Gielen S, Gabel G, Bergert H, Schuler G, Thiery J, Teupser D (2010) ANRIL expression is associated with atherosclerosis risk at chromosome 9p21. Arterioscler Thromb Vasc Biol 30(3):620–627

    Article  CAS  PubMed  Google Scholar 

  119. Bell RD, Long X, Lin M, Bergmann JH, Nanda V, Cowan SL, Zhou Q, Han Y, Spector DL, Zheng D et al (2014) Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. Arterioscler Thromb Vasc Biol 34(6):1249–1259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Boulberdaa M, Scott E, Ballantyne M, Garcia R, Descamps B, Angelini GD, Brittan M, Hunter A, McBride M, McClure J et al (2016) A role for the long noncoding RNA SENCR in commitment and function of endothelial cells. Mol Ther 24(5):978–990

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Kumarswamy R, Bauters C, Volkmann I, Maury F, Fetisch J, Holzmann A, Lemesle G, de Groote P, Pinet F, Thum T (2014) Circulating long noncoding RNA, LIPCAR, predicts survival in patients with heart failure. Circ Res 114(10):1569–1575

    Article  CAS  PubMed  Google Scholar 

  122. Wang K, Long B, Zhou LY, Liu F, Zhou QY, Liu CY, Fan YY, Li PF (2014) CARL lncRNA inhibits anoxia-induced mitochondrial fission and apoptosis in cardiomyocytes by impairing miR-539-dependent PHB2 downregulation. Nat Commun 5:3596

    PubMed  Google Scholar 

  123. Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y, Ikegawa S, Kamatani N, Hori M et al (2006) Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 51(12):1087–1099

    Article  CAS  PubMed  Google Scholar 

  124. Jiang Q, Shan K, Qun-Wang X, Zhou RM, Yang H, Liu C, Li YJ, Yao J, Li XM, Shen Y et al (2016) Long non-coding RNA-MIAT promotes neurovascular remodeling in the eye and brain. Oncotarget 7(31):49688–49698

    Article  PubMed  PubMed Central  Google Scholar 

  125. Liao J, He Q, Li M, Chen Y, Liu Y, Wang J (2016) LncRNA MIAT: myocardial infarction associated and more. Gene 578(2):158–161

    Article  CAS  PubMed  Google Scholar 

  126. Yan B, Yao J, Liu JY, Li XM, Wang XQ, Li YJ, Tao ZF, Song YC, Chen Q, Jiang Q (2015) lncRNA-MIAT regulates microvascular dysfunction by functioning as a competing endogenous RNA. Circ Res 116(7):1143–1156

    Article  CAS  PubMed  Google Scholar 

  127. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S et al (2013) Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152(3):570–583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, Macura K, Blass G, Kellis M, Werber M et al (2013) The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 24(2):206–214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Grote P, Herrmann BG (2013) The long non-coding RNA Fendrr links epigenetic control mechanisms to gene regulatory networks in mammalian embryogenesis. RNA Biol 10(10):1579–1585

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Collier SP, Collins PL, Williams CL, Boothby MR, Aune TM (2012) Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells. J Immunol 189(5):2084–2088

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Li H, Hao Y, Zhang D, Fu R, Liu W, Zhang X, Xue F, Yang R (2016) Aberrant expression of long noncoding RNA TMEVPG1 in patients with primary immune thrombocytopenia. Autoimmunity 49(7):496–502

    Article  CAS  PubMed  Google Scholar 

  132. Wang J, Peng H, Tian J, Ma J, Tang X, Rui K, Tian X, Wang Y, Chen J, Lu L et al (2016) Upregulation of long noncoding RNA TMEVPG1 enhances T helper type 1 cell response in patients with Sjogren syndrome. Immunol Res 64(2):489–496

    Article  CAS  PubMed  Google Scholar 

  133. Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, Chang HY, Brahic M, Kirkegaard K (2013) The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell 152(4):743–754

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Wang P, Xue Y, Han Y, Lin L, Wu C, Xu S, Jiang Z, Xu J, Liu Q, Cao X (2014) The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science 344(6181):310–313

    Article  CAS  PubMed  Google Scholar 

  135. Archer K, Broskova Z, Bayoumi AS, Teoh JP, Davila A, Tang Y, Su H, Kim IM (2015) Long non-coding RNAs as master regulators in cardiovascular diseases. Int J Mol Sci 16(10):23651–23667

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Sigdel KR, Cheng A, Wang Y, Duan L, Zhang Y (2015) The emerging functions of long noncoding RNA in immune cells: autoimmune diseases. J Immunol Res 2015:848790

    Article  PubMed  PubMed Central  Google Scholar 

  137. Krawczyk M, Emerson BM (2014) p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-kappaB complexes. eLife 3:e01776

    Article  PubMed  PubMed Central  Google Scholar 

  138. Wright PW, Huehn A, Cichocki F, Li H, Sharma N, Dang H, Lenvik TR, Woll P, Kaufman D, Miller JS et al (2013) Identification of a KIR antisense lncRNA expressed by progenitor cells. Genes Immun 14(7):427–433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Szell M, Danis J, Bata-Csorgo Z, Kemeny L (2016) PRINS, a primate-specific long non-coding RNA, plays a role in the keratinocyte stress response and psoriasis pathogenesis. Pflugers Arch 468(6):935–943

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Ng SY, Johnson R, Stanton LW (2012) Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J 31(3):522–533

    Article  CAS  PubMed  Google Scholar 

  141. Modarresi F, Faghihi MA, Patel NS, Sahagan BG, Wahlestedt C, Lopez-Toledano MA (2011) Knockdown of BACE1-AS nonprotein-coding transcript modulates beta-amyloid-related hippocampal neurogenesis. Int J Alzheimers Dis 2011:929042

    PubMed  PubMed Central  Google Scholar 

  142. Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, van der Brug MP, Wahlestedt C (2012) Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30(5):453–459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Zhang Y, Sun L, Xuan L, Pan Z, Li K, Liu S, Huang Y, Zhao X, Huang L, Wang Z et al (2016) Reciprocal changes of circulating long non-coding RNAs ZFAS1 and CDR1AS predict acute myocardial infarction. Sci Rep 6:22384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  144. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147(7):1537–1550

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Chalei V, Sansom SN, Kong L, Lee S, Montiel JF, Vance KW, Ponting CP (2014) The long non-coding RNA Dali is an epigenetic regulator of neural differentiation. eLife 3:e04530

    Article  PubMed  PubMed Central  Google Scholar 

  146. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Solda G, Simons C et al (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18(9):1433–1445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF (2010) Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation. BMC Neurosci 11:14

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  148. Kraus P, Sivakamasundari V, Lim SL, Xing X, Lipovich L, Lufkin T (2013) Making sense of Dlx1 antisense RNA. Dev Biol 376(2):224–235

    Article  CAS  PubMed  Google Scholar 

  149. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD (2006) The Evf-2 noncoding RNA is transcribed from the dlx-5/6 ultraconserved region and functions as a dlx-2 transcriptional coactivator. Genes Dev 20(11):1470–1484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Berghoff EG, Clark MF, Chen S, Cajigas I, Leib DE, Kohtz JD (2013) Evf2 (Dlx6as) lncRNA regulates ultraconserved enhancer methylation and the differential transcriptional control of adjacent genes. Development 140(21):4407–4416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  151. Airavaara M, Pletnikova O, Doyle ME, Zhang YE, Troncoso JC, Liu QR (2011) Identification of novel GDNF isoforms and cis-antisense GDNFOS gene and their regulation in human middle temporal gyrus of Alzheimer disease. J Biol Chem 286(52):45093–45102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Barry G, Briggs JA, Vanichkina DP, Poth EM, Beveridge NJ, Ratnu VS, Nayler SP, Nones K, Hu J, Bredy TW et al (2014) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry 19(4):486–494

    Article  CAS  PubMed  Google Scholar 

  153. Takahashi S, Ohtsuki T, SY Y, Tanabe E, Yara K, Kamioka M, Matsushima E, Matsuura M, Ishikawa K, Minowa Y et al (2003) Significant linkage to chromosome 22q for exploratory eye movement dysfunction in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 123B(1):27–32

    Article  PubMed  Google Scholar 

  154. Zhao X, Tang Z, Zhang H, Atianjoh FE, Zhao JY, Liang L, Wang W, Guan X, Kao SC, Tiwari V et al (2013) A long noncoding RNA contributes to neuropathic pain by silencing Kcna2 in primary afferent neurons. Nat Neurosci 16(8):1024–1031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Talkowski ME, Maussion G, Crapper L, Rosenfeld JA, Blumenthal I, Hanscom C, Chiang C, Lindgren A, Pereira S, Ruderfer D et al (2012) Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities. Am J Hum Genet 91(6):1128–1134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. PY V, Toutain J, Cappellen D, Delrue MA, Daoud H, El Moneim AA, Barat P, Montaubin O, Bonnet F, Dai ZQ et al (2012) A homozygous balanced reciprocal translocation suggests LINC00237 as a candidate gene for MOMO (macrosomia, obesity, macrocephaly, and ocular abnormalities) syndrome. Am J Med Genet A 158A(11):2849–2856

    Article  CAS  Google Scholar 

  157. Kerin T, Ramanathan A, Rivas K, Grepo N, Coetzee GA, Campbell DB (2012) A noncoding RNA antisense to moesin at 5p14.1 in autism. Sci Transl Med 4(128):128ra140

    Article  Google Scholar 

  158. Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, Zhang MQ, Sedel F, Jourdren L, Coulpier F et al (2010) A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J 29(18):3082–3093

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Zhang B, Arun G, Mao YS, Lazar Z, Hung G, Bhattacharjee G, Xiao X, Booth CJ, Wu J, Zhang C et al (2012) The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep 2(1):111–123

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, Lawrence JB (2009) An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 33(6):717–726

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Goff LA, Groff AF, Sauvageau M, Trayes-Gibson Z, Sanchez-Gomez DB, Morse M, Martin RD, Elcavage LE, Liapis SC, Gonzalez-Celeiro M et al (2015) Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 112(22):6855–6862

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, Oliver PL, Ponting CP (2014) The long non-coding RNA Paupar regulates the expression of both local and distal genes. EMBO J 33(4):296–311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz CC, Salinas RD, Zarabi H, Kriegstein AR, Lim DA (2015) The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. Cell Stem Cell 16(4):439–447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  164. Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC, Mattick JS (2009) Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA 15(11):2013–2027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  165. Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, Zhang D, Han T, Yang CS, Cunningham TJ et al (2014) An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 53(6):1005–1019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  166. Onoguchi M, Hirabayashi Y, Koseki H, Gotoh Y (2012) A noncoding RNA regulates the neurogenin1 gene locus during mouse neocortical development. Proc Natl Acad Sci U S A 109(42):16939–16944

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Lu L, Sun K, Chen X, Zhao Y, Wang L, Zhou L, Sun H, Wang H (2013) Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis. EMBO J 32(19):2575–2588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147(2):358–369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, Byron M, Monks B, Henry-Bezy M, Lawrence JB et al (2013) A long noncoding RNA mediates both activation and repression of immune response genes. Science 341(6147):789–792

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  170. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR et al (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21(2):198–206

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Yang F, Deng X, Ma W, Berletch JB, Rabaia N, Wei G, Moore JM, Filippova GN, Xu J, Liu Y et al (2015) The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation. Genome Biol 16:52

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  172. Berezney R, Coffey DS (1974) Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60(4):1410–1417

    Article  CAS  PubMed  Google Scholar 

  173. Nickerson J (2001) Experimental observations of a nuclear matrix. J Cell Sci 114(Pt 3):463–474

    CAS  PubMed  Google Scholar 

  174. Pathak RU, Mamillapalli A, Rangaraj N, Kumar RP, Vasanthi D, Mishra K, Mishra RK (2013) AAGAG repeat RNA is an essential component of nuclear matrix in Drosophila. RNA Biol 10(4):564–571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Zheng R, Shen Z, Tripathi V, Xuan Z, Freier SM, Bennett CF, Prasanth SG, Prasanth KV (2010) Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells. J Cell Sci 123(Pt 21):3734–3744

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Hall LL, Carone DM, Gomez AV, Kolpa HJ, Byron M, Mehta N, Fackelmayer FO, Lawrence JB (2014) Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes. Cell 156(5):907–919

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Ray MK, Wiskow O, King MJ, Ismail N, Ergun A, Wang Y, Plys AJ, Davis CP, Kathrein K, Sadreyev R et al (2016) CAT7 and cat7l long non-coding RNAs tune polycomb repressive complex 1 function during human and zebrafish development. J Biol Chem 291(37):19558–19572

    Article  CAS  PubMed  Google Scholar 

  178. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermuller J, Hofacker IL et al (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316(5830):1484–1488

    Article  CAS  PubMed  Google Scholar 

  179. Venters BJ, Pugh BF (2013) Genomic organization of human transcription initiation complexes. Nature 502(7469):53–58

    CAS  PubMed  PubMed Central  Google Scholar 

  180. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130(1):77–88

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK, Kurokawa R (2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454(7200):126–130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S et al (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465(7295):182–187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Sigova AA, Mullen AC, Molinie B, Gupta S, Orlando DA, Guenther MG, Almada AE, Lin C, Sharp PA, Giallourakis CC et al (2013) Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A 110(8):2876–2881

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Ong CT, Corces VG (2014) CTCF: an architectural protein bridging genome topology and function. Nat Rev Genet 15(4):234–246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Yao H, Brick K, Evrard Y, Xiao T, Camerini-Otero RD, Felsenfeld G (2010) Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev 24(22):2543–2555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Ebersole T, Kim JH, Samoshkin A, Kouprina N, Pavlicek A, White RJ, Larionov V (2011) tRNA genes protect a reporter gene from epigenetic silencing in mouse cells. Cell Cycle 10(16):2779–2791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Raab JR, Chiu J, Zhu J, Katzman S, Kurukuti S, Wade PA, Haussler D, Kamakaka RT (2012) Human tRNA genes function as chromatin insulators. EMBO J 31(2):330–350

    Article  CAS  PubMed  Google Scholar 

  188. Lunyak VV, Prefontaine GG, Nunez E, Cramer T, BG J, Ohgi KA, Hutt K, Roy R, Garcia-Diaz A, Zhu X et al (2007) Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science 317(5835):248–251

    Article  CAS  PubMed  Google Scholar 

  189. Lee S, Kopp F, Chang TC, Sataluri A, Chen B, Sivakumar S, Yu H, Xie Y, Mendell JT (2016) Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell 164(1–2):69–80

    Article  CAS  PubMed  Google Scholar 

  190. Misteli T (2007) Beyond the sequence: cellular organization of genome function. Cell 128(4):787–800

    Article  CAS  PubMed  Google Scholar 

  191. Dundr M, Misteli T (2010) Biogenesis of nuclear bodies. Cold Spring Harb Perspect Biol 2(12):a000711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Chen LL, Carmichael GG (2009) Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell 35(4):467–478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295(5558):1306–1311

    Article  CAS  PubMed  Google Scholar 

  194. Bouzinba-Segard H, Guais A, Francastel C (2006) Accumulation of small murine minor satellite transcripts leads to impaired centromeric architecture and function. Proc Natl Acad Sci U S A 103(23):8709–8714

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  195. Wong LH, Brettingham-Moore KH, Chan L, Quach JM, Anderson MA, Northrop EL, Hannan R, Saffery R, Shaw ML, Williams E et al (2007) Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere. Genome Res 17(8):1146–1160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Ohkuni K, Kitagawa K (2011) Endogenous transcription at the centromere facilitates centromere activity in budding yeast. Curr Biol 21(20):1695–1703

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  197. Topp CN, Zhong CX, Dawe RK (2004) Centromere-encoded RNAs are integral components of the maize kinetochore. Proc Natl Acad Sci U S A 101(45):15986–15991

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Blower MD (2016) Centromeric transcription regulates aurora-B localization and activation. Cell Rep 15(8):1624–1633

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Black BE, Cleveland DW (2011) Epigenetic centromere propagation and the nature of CENP-a nucleosomes. Cell 144(4):471–479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Quenet D, Dalal Y (2014) A long non-coding RNA is required for targeting centromeric protein a to the human centromere. eLife 3:e03254

    Article  PubMed  PubMed Central  Google Scholar 

  201. Liu H, Qu Q, Warrington R, Rice A, Cheng N, Yu H (2015) Mitotic transcription installs Sgo1 at centromeres to coordinate chromosome segregation. Mol Cell 59(3):426–436

    Article  CAS  PubMed  Google Scholar 

  202. Ting DT, Lipson D, Paul S, Brannigan BW, Akhavanfard S, Coffman EJ, Contino G, Deshpande V, Iafrate AJ, Letovsky S et al (2011) Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 331(6017):593–596

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  203. Greider CW, Blackburn EH (1985) Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. Cell 43(2 Pt 1):405–413

    Article  CAS  PubMed  Google Scholar 

  204. Smogorzewska A, de Lange T (2004) Regulation of telomerase by telomeric proteins. Annu Rev Biochem 73:177–208

    Article  CAS  PubMed  Google Scholar 

  205. Lundblad V (1998) Telomerase catalysis: a phylogenetically conserved reverse transcriptase. Proc Natl Acad Sci U S A 95(15):8415–8416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Hug N, Lingner J (2006) Telomere length homeostasis. Chromosoma 115(6):413–425

    Article  CAS  PubMed  Google Scholar 

  207. Blasco MA, Lee HW, Hande MP, Samper E, Lansdorp PM, DePinho RA, Greider CW (1997) Telomere shortening and tumor formation by mouse cells lacking telomerase RNA. Cell 91(1):25–34

    Article  CAS  PubMed  Google Scholar 

  208. Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J (2007) Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science 318(5851):798–801

    Article  CAS  PubMed  Google Scholar 

  209. Schoeftner S, Blasco MA (2008) Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II. Nat Cell Biol 10(2):228–236

    Article  CAS  PubMed  Google Scholar 

  210. Arnoult N, Van Beneden A, Decottignies A (2012) Telomere length regulates TERRA levels through increased trimethylation of telomeric H3K9 and HP1alpha. Nat Struct Mol Biol 19(9):948–956

    Article  CAS  PubMed  Google Scholar 

  211. Flynn RL, Cox KE, Jeitany M, Wakimoto H, Bryll AR, Ganem NJ, Bersani F, Pineda JR, Suva ML, Benes CH et al (2015) Alternative lengthening of telomeres renders cancer cells hypersensitive to ATR inhibitors. Science 347(6219):273–277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Porro A, Feuerhahn S, Delafontaine J, Riethman H, Rougemont J, Lingner J (2014) Functional characterization of the TERRA transcriptome at damaged telomeres. Nat Commun 5:5379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  213. Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149(4):819–831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  214. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106(23):9362–9367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  215. Hangauer MJ, Vaughn IW, McManus MT (2013) Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet 9(6):e1003569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  216. Meng L, Ward AJ, Chun S, Bennett CF, Beaudet AL, Rigo F (2015) Towards a therapy for Angelman syndrome by targeting a long non-coding RNA. Nature 518(7539):409–412

    Article  CAS  PubMed  Google Scholar 

  217. Shi L, Zhang Z, AM Y, Wang W, Wei Z, Akhter E, Maurer K, Costa Reis P, Song L, Petri M et al (2014) The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs. PLoS One 9(5):e93846

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  218. Muller N, Doring F, Klapper M, Neumann K, Schulte DM, Turk K, Schroder JO, Zeuner RA, Freitag-Wolf S, Schreiber S et al (2014) Interleukin-6 and tumour necrosis factor-alpha differentially regulate lincRNA transcripts in cells of the innate immune system in vivo in human subjects with rheumatoid arthritis. Cytokine 68(1):65–68

    Article  CAS  PubMed  Google Scholar 

  219. Shirasawa S, Harada H, Furugaki K, Akamizu T, Ishikawa N, Ito K, Ito K, Tamai H, Kuma K, Kubota S et al (2004) SNPs in the promoter of a B cell-specific antisense transcript, SAS-ZFAT, determine susceptibility to autoimmune thyroid disease. Hum Mol Genet 13(19):2221–2231

    Article  CAS  PubMed  Google Scholar 

  220. Lee CS, Ungewickell A, Bhaduri A, Qu K, Webster DE, Armstrong R, Weng WK, Aros CJ, Mah A, Chen RO et al (2012) Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts. Blood 120(16):3288–3297

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  221. Li R, Zhang L, Jia L, Duan Y, Li Y, Bao L, Sha N (2014) Long non-coding RNA BANCR promotes proliferation in malignant melanoma by regulating MAPK pathway activation. PLoS One 9(6):e100893

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  222. Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS, Perera RJ (2011) The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. Cancer Res 71(11):3852–3862

    Article  CAS  PubMed  Google Scholar 

  223. Maass PG, Rump A, Schulz H, Stricker S, Schulze L, Platzer K, Aydin A, Tinschert S, Goldring MB, Luft FC et al (2012) A misplaced lncRNA causes brachydactyly in humans. J Clin Invest 122(11):3990–4002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  224. Maicher A, Kastner L, Luke B (2012) Telomeres and disease: enter TERRA. RNA Biol 9(6):843–849

    Article  CAS  PubMed  Google Scholar 

  225. Temple IK, Shield JP (2002) Transient neonatal diabetes, a disorder of imprinting. J Med Genet 39(12):872–875

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  226. McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco M, Burghard C, Moradian A et al (2015) The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521(7551):232–236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  227. Ladd PD, Smith LE, Rabaia NA, Moore JM, Georges SA, Hansen RS, Hagerman RJ, Tassone F, Tapscott SJ, Filippova GN (2007) An antisense transcript spanning the CGG repeat region of FMR1 is upregulated in premutation carriers but silenced in full mutation individuals. Hum Mol Genet 16(24):3174–3187

    Article  CAS  PubMed  Google Scholar 

  228. Khalil AM, Faghihi MA, Modarresi F, Brothers SP, Wahlestedt C (2008) A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome. PLoS One 3(1):e1486

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  229. Merelo V, Durand D, Lescallette AR, Vrana KE, Hong LE, Faghihi MA, Bellon A (2015) Associating schizophrenia, long non-coding RNAs and neurostructural dynamics. Front Mol Neurosci 8:57

    Article  PubMed  PubMed Central  Google Scholar 

  230. Sahoo T, del Gaudio D, German JR, Shinawi M, Peters SU, Person RE, Garnica A, Cheung SW, Beaudet AL (2008) Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat Genet 40(6):719–721

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  231. Jong MT, Gray TA, Ji Y, Glenn CC, Saitoh S, Driscoll DJ, Nicholls RD (1999) A novel imprinted gene, encoding a RING zinc-finger protein, and overlapping antisense transcript in the Prader-Willi syndrome critical region. Hum Mol Genet 8(5):783–793

    Article  CAS  PubMed  Google Scholar 

  232. Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K (2001) The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum Mol Genet 10(23):2687–2700

    Article  CAS  PubMed  Google Scholar 

  233. Noor A, Whibley A, Marshall CR, Gianakopoulos PJ, Piton A, Carson AR, Orlic-Milacic M, Lionel AC, Sato D, Pinto D et al (2010) Disruption at the PTCHD1 locus on Xp22.11 in autism spectrum disorder and intellectual disability. Sci Transl Med 2(49):49ra68

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  234. Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M, Scherer SW (2002) The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a complex multi-transcript system. Genomics 80(3):283–294

    Article  CAS  PubMed  Google Scholar 

  235. Petazzi P, Sandoval J, Szczesna K, Jorge OC, Roa L, Sayols S, Gomez A, Huertas D, Esteller M (2013) Dysregulation of the long non-coding RNA transcriptome in a Rett syndrome mouse model. RNA Biol 10(7):1197–1203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  236. Hancarova M, Simandlova M, Drabova J, Mannik K, Kurg A, Sedlacek Z (2013) A patient with de novo 0.45 Mb deletion of 2p16.1: the role of BCL11A, PAPOLG, REL, and FLJ16341 in the 2p15-p16.1 microdeletion syndrome. Am J Med Genet A 161A(4):865–870

    Article  PubMed  Google Scholar 

  237. Arron JR, Winslow MM, Polleri A, Chang CP, Wu H, Gao X, Neilson JR, Chen L, Heit JJ, Kim SK et al (2006) NFAT dysregulation by increased dosage of DSCR1 and DYRK1A on chromosome 21. Nature 441(7093):595–600

    Article  CAS  PubMed  Google Scholar 

  238. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G III, Kenny PJ, Wahlestedt C (2008) Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 14(7):723–730

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  239. Eggermann T (2009) Silver-Russell and Beckwith-Wiedemann syndromes: opposite (epi)mutations in 11p15 result in opposite clinical pictures. Horm Res 71(Suppl 2):30–35

    CAS  PubMed  Google Scholar 

  240. Wevrick R, Kerns JA, Francke U (1994) Identification of a novel paternally expressed gene in the Prader-Willi syndrome region. Hum Mol Genet 3(10):1877–1882

    Article  CAS  PubMed  Google Scholar 

  241. Ounzain S, Micheletti R, Beckmann T, Schroen B, Alexanian M, Pezzuto I, Crippa S, Nemir M, Sarre A, Johnson R et al (2015) Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur Heart J 36(6):353–368a

    Article  PubMed  Google Scholar 

  242. van Dijk M, Visser A, Buabeng KM, Poutsma A, van der Schors RC, Oudejans CB (2015) Mutations within the LINC-HELLP non-coding RNA differentially bind ribosomal and RNA splicing complexes and negatively affect trophoblast differentiation. Hum Mol Genet 24(19):5475–5485

    Article  PubMed  CAS  Google Scholar 

  243. Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE (2010) Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 6(12):e1001233

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India

    Parna Saha, Shreekant Verma, Rashmi U. Pathak & Rakesh K. Mishra

Authors
  1. Parna Saha
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shreekant Verma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rashmi U. Pathak
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Rakesh K. Mishra
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Rashmi U. Pathak or Rakesh K. Mishra .

Editor information

Editors and Affiliations

  1. Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India

    M.R.S. Rao

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Nature Singapore Pte Ltd.

About this chapter

Cite this chapter

Saha, P., Verma, S., Pathak, R.U., Mishra, R.K. (2017). Long Noncoding RNAs in Mammalian Development and Diseases. In: Rao, M. (eds) Long Non Coding RNA Biology. Advances in Experimental Medicine and Biology, vol 1008. Springer, Singapore. https://doi.org/10.1007/978-981-10-5203-3_6

Download citation

Publish with us

Policies and ethics

Search

Navigation