This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
D. H. Ardell, C. A. Lozupone, and L. F. Landweber. Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea). Genetics, 165:1761–1777, 2003.
A. R. Cavalcanti, T. H. Clarke, and L. F. Landweber. MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates. Nucleic Acids Res., 33:D396–D398, 2005. (Database issue).
A. R. Cavalcanti and L. F. Landweber. Gene unscrambler for detangling scrambled genes in ciliates. Bioinformatics, 20:800–802, 2004.
D. L. Chalker, Fuller P., and M. C. Yao. Communication between parental and developing genomes during Tetrahymena nuclear differentiation is likely mediated by homologous RNAs. Genetics, 169:149–160, 2005.
D. L. Chalker and M. C. Yao. Non-Mendelian, heritable blocks to DNA rearrangement are induced by loading the somatic nucleus of Tetrahymena themophila with germ line-limited DNA. Mol. Cell Biol., 16:3658–3667, 1996.
D. L. Chalker and M. C. Yao. Nongenic, bidirectional transcription precedes and may promote developmental DNA deletion in Tetrahymena thermophila. Genes Dev., 15:1287–1298, 2001.
M. DuBois and D. M. Prescott. Scrambling of the actin I gene in two Oxytricha species. Proc. Natl. Acad. Sci. USA, 92:3888–3892, 1995.
L. M. Epstein and J. D. Forney. Mendelian and non-mendelian mutations affecting surface antigen expression in Paramecium tetraurelia. Mol. Cell Biol., 4:1583–1590, 1984.
O. Garnier, V. Serrano, S. Duharcourt, and E. Meyer. RNA-mediated programming of developmental genome rearrangements in Paramecium tetraurelia. Mol. Cell Biol., 24:7370–7379, 2004.
A. Gratias and M. Bétermier. Developmentally programmed excision of internal DNA sequences in Paramecium aurelia. Biochimie, 83:1009–1022, 2001.
D. C. Hoffman and D. M. Prescott. The germline gene encoding DNA polymerase alpha in the hypotrichous ciliate Oxytricha nova is extremely scrambled. Nucleic Acids Res., 24:3337–3340, 1996.
S. Juranek, S. Rupprecht, J. Postberg, and H. J. Lipps. snRNA specify DNA-sequences but are not sufficient for their correct excision during macronuclear development. Submitted, 2005.
S. Kuo, W. J. Chang, and L. F. Landweber. Complex germline architecture: Two genes intertwined on two loci. (Submitted), 2005.
L. F. Landweber, T. C. Kuo, and E. A. Curtis. Evolution and assembly of an extremely scrambled gene. Proc. Natl. Acad. Sci. USA, 97:3298–3303, 2000.
A. Le Mouël, A. Butler, F. Caron, and E. Meyer. Developmentally regulated chromosome fragmentation linked to imprecise elimination of repeated sequences in paramecia. Eukaryot Cell, 2:1076–1090, 2003.
J. L. Mitcham, A. J. Lynn, and D. M. Prescott. Analysis of a scrambled gene: the gene encoding alpha-telomere-binding protein in Oxytricha nova. Genes Dev., 6:788–800, 1992.
K. Mochizuki, N. A. Fine, T. Fujisawa, and M. A. Gorovsky. Analysis of a piwirelated gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell, 110:689–699, 2002.
K. Mochizuki and M. A. Gorovsky. RNA polymerase II localizes in Tetrahymena thermophila meiotic micronuclei when micronuclear transcription associated with genome rearrangement occurs. Eukaryot Cell, 3:1233–1240, 2004.
K. Mochizuki and M. A. Gorovsky. Small RNAs in genome rearrangement in Tetrahymena. Curr. Opin. Genet. Dev., 14:181–187, 2004.
K. Mochizuki and M. A. Gorovsky. A dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase. Genes Dev., 19:77–89, 2005.
D. M. Prescott. The DNA of ciliated protozoa. Microbiol. Rev., 58:233–267, 1994.
D. M. Prescott. Genome gymnastics: unique modes of DNA evolution and processing in ciliates. Nat. Rev. Genet., 1:191–198, 2000.
D.M. Prescott, M. DuBois, Internal eliminated segments (IESs) of Oxytrichidae. J. Eukariot. Microbiol. 43 (1996) 432–441.
D. M. Prescott, A. Ehrenfeucht, and G. Rozenberg. Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates. J. Theor. Biol., 222:323–330, 2003.
K. Williams, T. G. Doak, and G. Herrick. Developmental precise excision of Oxytricha trifallax telomere-bearing elements and formation of circles closed by a copy of the flanking target duplication. EMBO J., 12:4593–4601, 1993.
M. C. Yao, P. Fuller, and X. Xi. Programmed DNA deletion as an RNA-guided system of genome defense. Science, 300:1581–1584, 2003.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Cavalcanti, A.R.O., Landweber, L.F. (2006). Insights into a Biological Computer: Detangling Scrambled Genes in Ciliates. In: Chen, J., Jonoska, N., Rozenberg, G. (eds) Nanotechnology: Science and Computation. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-30296-4_22
Download citation
DOI: https://doi.org/10.1007/3-540-30296-4_22
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-30295-7
Online ISBN: 978-3-540-30296-4
eBook Packages: Computer ScienceComputer Science (R0)