H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability

Nature Cell Biology

Volumn 9, Issue 1, 2007, Pages 25-35

  Peng, Jamy C ^a,b   Karpen, Gary H ^a,b  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COHESIN; HISTONE H3; LIGASE; LYSINE; REPETITIVE DNA; RIBOSOME DNA; SATELLITE DNA;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL NUCLEUS; CELL STRUCTURE; CHROMATIN; CHROMATIN STRUCTURE; CHROMOSOME NOR; CONTROLLED STUDY; DNA SYNTHESIS; DROSOPHILA; GENE SILENCING; GENETIC STABILITY; GENOMIC INSTABILITY; HETEROCHROMATIN; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN METHYLATION; REGULATORY MECHANISM; RNA INTERFERENCE; STRUCTURE ANALYSIS; WILD TYPE;

ANIMALS; CELL CYCLE PROTEINS; CELL NUCLEOLUS; CHROMOSOMAL PROTEINS, NON-HISTONE; DNA METHYLATION; DNA, RIBOSOMAL; DNA, SATELLITE; DROSOPHILA; DROSOPHILA PROTEINS; HETEROCHROMATIN; HISTONES; MODELS, GENETIC; NUCLEAR PROTEINS; PROTEIN INHIBITORS OF ACTIVATED STAT; REPRESSOR PROTEINS; RNA INTERFERENCE;

EID: 33845866637     PISSN: 14657392     EISSN: None     Source Type: Journal    
DOI: 10.1038/ncb1514     Document Type: Article

References (48)

1. Francastel, C., Schubeler, D., Martin, D. I. & Groudine, M. Nuclear compartmentalization and gene activity. Nature Rev. Mol. Cell Biol. 1, 137-143 (2000).
2. Cremer, T. & Cremer, C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Rev. Genet. 2, 292-301 (2001).
3. John, B. The biology of heterochromatin. in Heterochromatin: Molecular and Structural Aspects (ed. Verma, R. S.) 1-147 (Cambridge University Press, Cambridge, 1988).
4. Martin, C. & Zhang, Y. The diverse functions of histone lysine methylation. Nature Rev. Mol. Cell Biol. 6, 838-849 (2005).
5. Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074-1080 (2001).
6. Muller, H. J. Types of visible variations induced by X-rays in Drosophila. J. Genet. 22, 299-334 (1930).
7. Schotta, G., Ebert, A., Dorn, R. & Reuter, G. Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin. Cell Dev. Biol. 14, 67-75 (2003).
8. Pal-Bhadra, M. et al. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science 303, 669-672 (2004).
9. Grewal, S. I. & Moazed, D. Heterochromatin and epigenetic control of gene expression. Science 301, 798-802 (2003).
10. Karpen, G. H., Schaefer, J. E. & Laird, C. D. A Drosophila rRNA gene located in euchromatin is active in transcription and nucleolus formation. Genes Dev. 2, 1745-1763 (1988).
11. Santoro, R., Li, J. & Grummt, I. The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription. Nature Genet. 32, 393-396 (2002).
12. Pikaard, C. S. The epigenetics of nucleolar dominance. Trends Genet. 16, 495-500 (2000).
13. Hawley, R. S. & Marcus, C. H. Recombinational controls of rDNA redundancy in Drosophila. Annu. Rev. Genet. 23, 87-120 (1989).
14. Blander, G. & Guarente, L. The Sir2 family of protein deacetylases. Annu. Rev. Biochem. 73, 417-435 (2004).
15. Tollervey, D., Lehtonen, H., Jansen, R., Kern, H. & Hurt, E. C. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell 72, 443-457 (1993).
16. Spradling, A. & Orr-Weaver, T. Regulation of DNA replication during Drosophila development. Annu. Rev. Genet. 21, 373-403 (1987).
17. Schotta, G. et al. Central role of Drosophila SU(VAR)3-9 in histone H3K9 methylation and heterochromatic gene silencing. EMBO J. 21, 1121-1131 (2002).
18. Hirt, B. Selective extraction of polyoma DNA from infected mouse cell cultures. J. Mol. Biol. 26, 365-369 (1967).
19. Pont, G., Degroote, F. & Picard, G. Some extrachromosomal circular DNAs from Drosophila embryos are homologous to tandemly repeated genes. J. Mol. Biol. 195, 447-451 (1987).
20. Aravin, A. A. et al. The small RNA profile during Drosophila melanogaster development. Dev. Cell 5, 337-350 (2003).
21. Lin, Y. H. & Keil, R. L. Mutations affecting RNA polymerase I-stimulated exchange and rDNA recombination in yeast. Genetics 127, 31-38 (1991).
22. Cohen, S., Yacobi, K. & Segal, D. Extrachromosomal circular DNA of tandemly repeated genomic sequences in Drosophila. Genome Res 13, 1133-1145 (2003).
23. Cohen, Z., Bacharach, E. & Lavi, S. Mouse major satellite DNA is prone to eccDNA formation via DNA Ligase IV-dependent pathway. Oncogene 25, 4515-4524 (2006).
24. Kobayashi, T. & Ganley, A. R. Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science 309, 1581-1584 (2005).
25. Nonaka, N. et al. Recruitment of cohesin to heterochromatic regions by Swi6/HP1 in fission yeast. Nature Cell Biol. 4, 89-93 (2002).
26. Losada, A., Hirano, M. & Hirano, T. Identification of Xenopus SMC protein complexes required for sister chromatid†cohesion. Genes Dev. 12, 1986-1997 (1998).
27. Vakoc, C. R., Mandat, S. A., Olenchock, B. A. & Blobel, G. A. Histone H3 lysine 9 methylation and HP1γ are associated with transcription elongation through mammalian chromatin. Mol Cell 19, 381-391 (2005).
28. Sullivan, B. A. & Karpen, G. H. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nature Struct. Mol. Biol. 11, 1076-1083 (2004).
29. Jackson, P. K. A new RING for SUMO: Wrestling transcriptional responses into nuclear bodies with PIAS family E3 SUMO ligases. Genes Dev. 15, 3053-3058 (2001).
30. Hari, K. L., Cook, K. R. & Karpen, G. H. The Drosophila Su(var)2-10 locus encodes a member of the PIAS protein family and regulates chromosome structure and function. Genes Dev. 15, 1334-1348 (2001).
31. Schotta, G. et al. A silencing pathway to induce H3K9 and H4K20 trimethylation at constitutive heterochromatin. Genes Dev. 18, 1251-1262 (2004).
32. Lee, Y. S. et al. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell 117, 69-81 (2004).
33. Cam, H. P. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nature Genet. 37, 809-819 (2005).
34. Peters, A. H. et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107, 323-337 (2001).
35. McKee, B. D. & Karpen, G. H. Drosophila ribosomal RNA genes function as an X-Y pairing site during male meiosis. Cell 61, 61-72 (1990).
36. Karpen, G. H., Le, M. H. & Le, H. Centric heterochromatin and the efficiency of achiasmate disjunction in Drosophila female meiosis. Science 273, 118-122 (1996).
37. Dernburg, A. F., Sedat, J. W. & Hawley, R. S. Direct evidence of a role for heterochromatin in meiotic chromosome segregation. Cell 86, 135-146 (1996).
38. Cartwright, I. L. et al. Analysis of Drosophila chromatin structure in vivo. Methods Enzymol. 304, 462-496 (1999).
39. Critchlow, S. E., Bowater, R. P. & Jackson, S. P. Mammalian DNA double-strand break repair protein XRCC4 interacts with DNA ligase IV. Curr. Biol. 7, 588-598 (1997).
40. Glaser, R. L., Karpen, G. H. & Spradling, A. C. Replication forks are not found in a Drosophila minichromosome demonstrating a gradient of polytenization. Chromosoma 102, 15-19 (1992).
41. Ivessa, A. S., Zhou, J. Q. & Zakian, V. A. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell 100, 479-489 (2000).
42. Westphal, T. & Reuter, G. Recombinogenic effects of suppressors of position-effect variegation in Drosophila. Genetics 160, 609-621 (2002).
43. Kaeberlein, M., McVey, M. & Guarente, L. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev. 13, 2570-2580 (1999).
44. Osipovich, O. et al. Targeted inhibition of V(D)J recombination by a histone methyltransferase. Nature Immunol. 5, 309-316 (2004).
45. Peters, A. H. F. M. et al. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12, 1577-1589 (2003).
46. Dorsett, D. et al. Effects of sister chromatid cohesion proteins on cut gene expression during wing development in Drosophila. Development 132, 4743-4753 (2005).
47. Austin, R. J., Orr-Weaver, T. L. & Bell, S. P. Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element. Genes Dev. 13, 2639-2649 (1999).
48. Kuschak, T. I., Kuschak, B. C., Smith, G. M., Wright, J. A. & Mai, S. Isolation of extrachromosomal elements by histone immunoprecipitation. Biotechniques 30, 1064-1068, 1070-1072 (2001).