Chromatin landscape: Methylation beyond transcription

Epigenetics

Volumn 6, Issue 1, 2011, Pages 9-15

  Black, Joshua C ^a   Whetstine, Johnathan R ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Chromatin; Euchromatin; H3K9; H3K9me3; Heterochromatin; Histone; Histone demethylase; Histone demethylases; Histone methyltransferase; HP1; KDM; KMT; Lamin; Lysine methylation

Indexed keywords

CHROMOSOME PROTEIN; DNA; HETEROCHROMATIN 1; HISTONE; HISTONE 3 LYSINE 9; HISTONE H2A; HISTONE H2B; HISTONE H3; HISTONE H4; LAMIN A; LAMIN B; LAMIN B1; LAMIN B2; LAMIN C; RNA; UNCLASSIFIED DRUG; HETEROCHROMATIN SPECIFIC NONHISTONE CHROMOSOMAL PROTEIN HP 1; HETEROCHROMATIN-SPECIFIC NONHISTONE CHROMOSOMAL PROTEIN HP-1; NONHISTONE PROTEIN;

ARTICLE; CHROMATIN; GENETIC TRANSCRIPTION; HUMAN; METHYLATION; NEOPLASM; ANIMAL; GENE DUPLICATION; GENETICS; METABOLISM; PHYSIOLOGY; PROTEIN PROCESSING; REVIEW;

ANIMALS; CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; DNA; GENE DUPLICATION; HISTONES; HUMANS; METHYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; TRANSCRIPTION, GENETIC;

EID: 78651246115     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.6.1.13331     Document Type: Article

References (60)

1. Trojer P, Reinberg D. Facultative heterochromatin: is there a distinctive molecular signature? Mol Cell 2007; 28:1-13.
2. Kouzarides T. Chromatin modifications and their function. Cell 2007; 128:693-705.
3. Taddei A, Hediger F, Neumann FR, Gasser SM. The function of nuclear architecture: a genetic approach. Annu Rev Genet 2004; 38:305-345.
4. Shumaker DK, Dechat T, Kohlmaier A, Adam SA, Bozovsky MR, Erdos MR, et al. Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. Proc Natl Acad Sci USA 2006; 103:8703-8708.
5. Horn PJ, Peterson CL. Molecular biology. Chromatin higher order folding-wrapping up transcription. Science 2002; 297:1824-1827
6. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129:823-837
7. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007; 448:553-560.
8. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 2008; 40:897-903.
9. Brinkman AB, Roelofsen T, Pennings SW, Martens JH, Jenuwein T, Stunnenberg HG. Histone modification patterns associated with the human X chromosome. EMBO Rep 2006; 7:628-634.
10. Vakoc CR, Mandat SA, Olenchock BA, Blobel GA. Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. Mol Cell 2005; 19:381-391.
11. Shi Y, Whetstine JR. Dynamic regulation of histone lysine methylation by demethylases. Mol Cell 2007; 25:1-14.
12. Trojer P, Zhang J, Yonezawa M, Schmidt A, Zheng H, Jenuwein T, et al. Dynamic histone H1 isotype 4 methylation and demethylation by histone lysine methyltransferase G9a/KMT1C and the jumonji domain-containing JMJD2/KDM4 proteins. J Biol Chem 2009; 284:8395-8405.
13. Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, et al. Reversal of histone lysine trimethyl-ation by the JMJD2 family of histone demethylases. Cell 2006; 125:467-481.
14. Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genom 2009; 10:143.
15. Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet 2009; 41:246-250.
16. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008; 453:948-951.
17. Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, Tamir I, et al. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 2009; 19:221-233.
18. Regha K, Sloane MA, Huang R, Pauler FM, Warczok KE, Melikant B, et al. Active and repressive chromatin are interspersed without spreading in an imprinted gene cluster in the mammalian genome. Mol Cell 2007; 27:353-366.
19. Narita M, Nunez S, Heard E, Narita M, Lin AW, Hearn SA, et al. Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell 2003; 113:703-716.
20. Braig M, Lee S, Loddenkemper C, Rudolph C, Peters AH, Schlegelberger B, et al. Oncogene-induced senescence as an initial barrier in lymphoma development. Nature 2005; 436:660-665.
21. Kwon SH, Workman JL. The heterochromatin protein 1 (HP1) family: put away a bias toward HP1. Mol Cells 2008; 26:217-227
22. Ayoub N, Jeyasekharan AD, Bernal JA, Venkitaraman AR. HP1beta mobilization promotes chromatin changes that initiate the DNA damage response. Nature 2008; 453:682-686.
23. Dialynas GK, Terjung S, Brown JP, Aucott RL, Baron-Luhr B, Singh PB, et al. Plasticity of HP1 proteins in mammalian cells. J Cell Sci 2007; 120:3415-3424.
24. Minc E, Allory Y, Worman HJ, Courvalin JC, Buendia B. Localization and phosphorylation of HP1 proteins during the cell cycle in mammalian cells. Chromosoma 1999; 108:220-234.
25. Prasanth SG, Prasanth KV, Siddiqui K, Spector DL, Stillman B. Human Orc2 localizes to centrosomes, centromeres and heterochromatin during chromosome inheritance. EMBO J 2004; 23:2651-2663.
26. Schott S, Coustham V, Simonet T, Bedet C, Palladino F. Unique and redundant functions of C. elegans HP1 proteins in post-embryonic development. Dev Biol 2006; 298:176-187
27. Smothers JF, Henikoff S. The hinge and chromo shadow domain impart distinct targeting of HP1-like proteins. Mol Cell Biol 2001; 21:2555-2569.
28. Chen ES, Zhang K, Nicolas E, Cam HP, Zofall M, Grewal SI. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 2008; 451:734-737.
29. Chen ES, Zhang K, Nicolas E, Cam HP, Zofall M, Grewal SI. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 2008; 451:734-737.
30. Grewal SI, Jia S. Heterochromatin revisited. Nat Rev Genet 2007; 8:35-46.
31. Hayashi MT, Takahashi TS, Nakagawa T, Nakayama J, Masukata H. The heterochromatin protein Swi6/HP1 activates replication origins at the pericentromeric region and silent mating-type locus. Nat Cell Biol 2009; 11:357-362
32. Quivy JP, Gerard A, Cook AJ, Roche D, Almouzni G. The HP1-p150/CAF-1 interaction is required for pericentric heterochromatin replication and S-phase progression in mouse cells. Nat Struct Mol Biol 2008; 15:972-979.
33. Okada Y, Suzuki T, Sunden Y, Orba Y, Kose S, Imamoto N, et al. Dissociation of heterochromatin protein 1 from lamin B receptor induced by human polyomavirus agnoprotein: role in nuclear egress of viral particles. EMBO Rep 2005; 6:452-457
34. Schwaiger M, Kohler H, Oakeley EJ, Stadler MB, Schubeler D. Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome. Genome Res 2010; 20:771-780.
35. Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, et al. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci USA 2010; 107:139-144.
36. Karnani N, Taylor CM, Malhotra A, Dutta A. Genomic study of replication initiation in human chromosomes reveals the influence of transcription regulation and chromatin structure on origin selection. Mol Biol Cell 2010; 21:393-404.
37. MacAlpine HK, Gordan R, Powell SK, Hartemink AJ, MacAlpine DM. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Res 2010; 20:201-211.
38. Dimitrova DS, Berezney R. The spatio-temporal organization of DNA replication sites is identical in primary, immortalized and transformed mammalian cells. J Cell Sci 2002; 115:4037-4051.
39. Kennedy BK, Barbie DA, Classon M, Dyson N, Harlow E. Nuclear organization of DNA replication in primary mammalian cells. Genes Dev 2000; 14:2855-2868.
40. Schulze JM, Jackson J, Nakanishi S, Gardner JM, Hentrich T, Haug J, et al. Linking cell cycle to histone modifications: SBF and H2B monoubiquitina-tion machinery and cell cycle regulation of H3K79 dimethylation. Mol Cell 2009; 35:626-641.
41. Bracken AP, Pasini D, Capra M, Prosperini E, Colli E, Helin K. EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J 2003; 22:5323-5335.
42. MacAlpine DM, Rodriguez HK, Bell SP. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 2004; 18:3094-3105.
43. Mendez J. Temporal regulation of DNA replication in mammalian cells. Crit Rev Biochem Mol Biol 2009; 44:343-351.
44. Cimbora DM, Schubeler D, Reik A, Hamilton J, Francastel C, Epner EM, et al. Long-distance control of origin choice and replication timing in the human beta-globin locus are independent of the locus control region. Mol Cell Biol 2000; 20:5581-5591.
45. Schubeler D, Francastel C, Cimbora DM, Reik A, Martin DI, Groudine M. Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human beta-globin locus. Genes Dev 2000; 14:940-950.
46. Deal RB, Henikoff JG, Henikoff S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 2010; 328:1161-1164.
47. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, et al. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 2008; 6:245.
48. Chi P, Allis CD, Wang GG. Covalent histone modifications-miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 2010; 10:457-469.
49. Lim S, Metzger E, Schule R, Kirfel J, Buettner R. Epigenetic regulation of cancer growth by histone demethylases. Int J Cancer 2010; 127:1991-1998.
50. Henning SM, Swendseid ME, Coulson WF. Male rats fed methyl- and folate-deficient diets with or without niacin develop hepatic carcinomas associated with decreased tissue NAD concentrations and altered poly(ADP-ribose) polymerase activity. J Nutr 1997; 127:30-36.
51. Peters AH, O'Carroll D, Scherthan H, Mechtler K, Sauer S, Schofer C, et al. Loss of the Suv39 h histone me thy ltransfe rases impairs mammalian heterochromatin and genome stability. Cell 2001; 107:323-337
52. Northcott PA, Nakahara Y, Wu X, Feuk L, Ellison DW, Croul S, et al. Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Nat Genet 2009; 41:465-472.
53. Kondo Y, Shen L, Ahmed S, Boumber Y, Sekido Y, Haddad BR, et al. Down regulation of histone H3 lysine 9 methyltransferase G9a induces centrosome disruption and chromosome instability in cancer cells. PLoS One 2008; 3:2037.
54. Kleer CG, Cao Q, Varambally S, Shen R, Ota I, Tomlins SA, et al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc Natl Acad Sci USA 2003; 100:11606-11611.
55. Varambally S, Dhanasekaran SM, Zhou M, Barrette TR, Kumar-Sinha C, Sanda MG, et al. The poly-comb group protein EZH2 is involved in progression of prostate cancer. Nature 2002; 419:624-629.
56. van Haaften G, Dalgliesh GL, Davies H, Chen L, Bignell G, Greenman C, et al. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nat Genet 2009; 41:521-523.
57. Zink D, Fischer AH, Nickerson JA. Nuclear structure in cancer cells. Nat Rev Cancer 2004; 4:677-687
58. Willis ND, Cox TR, Rahman-Casans SF, Smits K, Przyborski SA, van den Brandt P, et al. Lamin A/C is a risk biomarker in colorectal cancer. PLoS One 2008; 3:2988.
59. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009; 326:289-293.
60. Lee BM, Mahadevan LC. Stability of histone modifications across mammalian genomes: implications for 'epigenetic' marking. J Cell Biochem 2009; 108:22-34.