A Computational Model for Histone Mark Propagation Reproduces the Distribution of Heterochromatin in Different Human Cell Types

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Schwämmle, Veit ^a   Jensen, Ole Nørregaard ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE;

ARTICLE; CD4 LYMPHOCYTE COUNT; CHEMICAL PHENOMENA; CHROMOSOME 1; CHROMOSOME REARRANGEMENT; COMPUTER MODEL; COMPUTER SIMULATION; CONTROLLED STUDY; EUCHROMATIN; GENE INACTIVATION; GENETIC TRANSCRIPTION; HELA CELL; HETEROCHROMATIN; HISTONE MODIFICATION; HUMAN; HUMAN CELL; NUCLEATION SITE;

CD4-POSITIVE T-LYMPHOCYTES; CELL LINE; CHROMOSOMES, HUMAN; EUCHROMATIN; HETEROCHROMATIN; HISTONES; HUMANS; METHYLATION; MODELS, BIOLOGICAL; NUCLEOSOMES;

EID: 84884377635     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0073818     Document Type: Article

References (74)

1. Fodor BD, Kubicek S, Yonezawa M, O'Sullivan RJ, Sengupta R, et al. (2006) Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells. Genes Dev 20: 1557-1562.
2. Dialynas GK, Vitalini MW, Wallrath LL, (2008) Linking Heterochromatin Protein 1 (HP1) to cancer progression. Mutat Res 647: 13-20.
3. Norwood LE, Moss TJ, Margaryan NV, Cook SL, Wright L, et al. (2006) A requirement for dimerization of HP1Hsα in suppression of breast cancer invasion. J Biol Chem 281: 18668-18676.
4. Cloos PAC, Christensen J, Agger K, Maiolica A, Rappsilber J, et al. (2006) The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3. Nature 442: 307-311.
5. Dodd IB, MicheelsenMA, Sneppen K, Thon G, (2007) Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129: 813-822.
6. Sneppen K, Micheelsen MA, Dodd IB, (2008) Ultrasensitive gene regulation by positive feedback loops in nucleosome modification. Mol Syst Biol 4: 182.
7. Micheelsen MA, Mitarai N, Sneppen K, Dodd IB, (2010) Theory for the stability and regulation of epigenetic landscapes. Phys Biol 7: 026010.
8. Sedighi M, Sengupta AM, (2007) Epigenetic chromatin silencing: bistability and front propagation. Phys Biol 4: 246-255.
9. Gils C, Wrana JL, Salem WKA (2009) A quantum spin approach to histone dynamics. arXiv: 0912.4465.
10. Angel A, Song J, Dean C, Howard M, (2011) A Polycomb-based switch underlying quantitative epigenetic memory. Nature 476: 105-108.
11. Hathaway NA, Bell O, Hodges C, Miller EL, Neel DS, et al. (2012) Dynamics and memory of heterochromatin in living cells. Cell 149: 1447-1460.
12. Hall IM, Shankaranarayana GD, Noma KI, Ayoub N, Cohen A, et al. (2002) Establishment and maintenance of a heterochromatin domain. Science 297: 2232-2237.
13. Grewal SIS, Jia S, (2007) Heterochromatin revisited. Nat Rev Genet 8: 35-46.
14. Sugiyama T, Cam H, Verdel A, Moazed D, Grewal SIS, (2005) RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc Natl Acad Sci 102: 152-157.
15. Noma K, Sugiyama T, Cam H, Verdel A, Zofall M, et al. (2004) RITS acts in cis to promote RNA interference-mediated transcriptional and post-transcriptional silencing. Nat Genet 36: 1174-1180.
16. Slotkin RK, Martienssen R, (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: 272-285.
17. Martens JHA, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, et al. (2005) The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 24: 800-812.
18. Kondo Y, Issa JPJ, (2003) Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells. J Biol Chem 278: 27658-27662.
19. Cam HP, Sugiyama T, Chen ES, Chen X, FitzGerald PC, et al. (2005) Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat Genet 37: 809-819.
20. Taft RJ, Pheasant M, Mattick JS, (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays 29: 288-299.
21. Mattick JS, (2007) A new paradigm for developmental biology. J Exp Biol 210: 1526-1547.
22. Bock C, Walter J, Paulsen M, Lengauer T, (2007) CpG island mapping by epigenome prediction. PLoS Comput Biol 3: e110.
23. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.
24. Roh TY, Cuddapah S, Zhao K, (2005) Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 19: 542-552.
25. Thomson JP, Skene PJ, Selfridge J, Clouaire T, Guy J, et al. (2010) CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464: 1082-1086.
26. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
27. de Wit E, van Steensel B, (2009) Chromatin domains in higher eukaryotes: insights from genomewide mapping studies. Chromosoma 118: 25-36.
28. Jenuwein T, (2001) Re-SET-ting heterochromatin by histone methyltransferases. Trends in Cell Biology 11: 266-273.
29. Peters AH, Kubicek S, Mechtler K, O'Sullivan RJ, Derijck AA, et al. (2003) Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Molecular Cell 12: 1577-1589.
30. Rice JC, Briggs SD, Ueberheide B, Barber CM, Shabanowitz J, et al. (2003) Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Molecular Cell 12: 1591-1598.
31. Grewal SIS, Moazed D, (2003) Heterochromatin and epigenetic control of gene expression. Science 301: 798-802.
32. Maison C, Almouzni G, (2004) HP1 and the dynamics of heterochromatin maintenance. Nat Rev Mol Cell Biol 5: 296-304.
33. Schotta G, Ebert A, Krauss V, Fischer A, Hoffmann J, et al. (2002) Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J 21: 1121-1131.
34. James TC, Eissenberg JC, Craig C, Dietrich V, Hobson A, et al. (1989) Distribution patterns of HP1, a heterochromatin-associated nonhistone chromosomal protein of Drosophila. Eur J Cell Biol 50: 170-180.
35. Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T, (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410: 116-120.
36. Czvitkovich S, Sauer S, Peters AH, Deiner E, Wolf A, et al. (2001) Over-expression of the SUV39H1 histone methyltransferase induces altered proliferation and differentiation in transgenic mice. Mech Dev 107: 141-153.
37. Aagaard L, Laible G, Selenko P, Schmid M, Dorn R, et al. (1999) Functional mammalian homologues of the Drosophila PEV-modifier Su(var)3-9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J 18: 1923-1938.
38. Estéve PO, Chin HG, Smallwood A, Feehery GR, Gangisetty O, et al. (2006) Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev 20: 3089-3103.
39. Smallwood A, Estve PO, Pradhan S, Carey M, (2007) Functional cooperation between HP1 and DNMT1 mediates gene silencing. Genes Dev 21: 1169-1178.
40. Fuks F, Hurd PJ, Deplus R, Kouzarides T, (2003) The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res 31: 2305-2312.
41. Zhang CL, McKinsey TA, Olson EN, (2002) Association of class II histone deacetylases with heterochromatin protein 1: potential role for histone methylation in control of muscle differentiation. Mol Cell Biol 22: 7302-7312.
42. Douarin BL, Nielsen AL, Garnier JM, Ichinose H, Jeanmougin F, et al. (1996) A possible involvement of TIF1 alpha and TIF1 beta in the epigenetic control of transcription by nuclear receptors. EMBO J 15: 6701-6715.
43. Gaszner M, Felsenfeld G, (2006) Insulators: exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet 7: 703-713.
44. Nightingale KP, Gendreizig S, White DA, Bradbury C, Hollfelder F, et al. (2007) Cross-talk between histone modifications in response to histone deacetylase inhibitors: MLL4 links histone H3 acetylation and histone H3K4 methylation. J Biol Chem 282: 4408-4416.
45. Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, et al. (2005) Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol 3: e328.
46. West AG, Huang S, Gaszner M, Litt MD, Felsenfeld G, (2004) Recruitment of histone modifications by USF proteins at a vertebrate barrier element. Mol Cell 16: 453-463.
47. Chiu YH, Yu Q, Sandmeier JJ, Bi X, (2003) A targeted histone acetyltransferase can create a sizable region of hyperacetylated chromatin and counteract the propagation of transcriptionally silent chromatin. Genetics 165: 115-125.
48. Donze D, Kamakaka RT, (2002) Braking the silence: how heterochromatic gene repression is stopped in its tracks. Bioessays 24: 344-349.
49. Pikaart MJ, Recillas-Targa F, Felsenfeld G, (1998) Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators. Genes Dev 12: 2852-2862.
50. Kimura A, Horikoshi M, (2004) Partition of distinct chromosomal regions: negotiable border and fixed border. Genes Cells 9: 499-508.
51. Wang J, Lunyak VV, Jordan IK, (2012) Genome-wide prediction and analysis of human chromatin boundary elements. Nucleic Acids Res 40: 511-529.
52. Mutskov V, Felsenfeld G, (2004) Silencing of transgene transcription precedes methylation of promoter DNA and histone H3 lysine 9. EMBO J 23: 138-149.
53. Zegerman P, Canas B, Pappin D, Kouzarides T, (2002) Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex. J Biol Chem 277: 11621-11624.
54. Nishioka K, Chuikov S, Sarma K, Erdjument-Bromage H, Allis CD, et al. (2002) Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev 16: 479-489.
55. Taddei A, Maison C, Roche D, Almouzni G, (2001) Reversible disruption of pericentric heterochromatin and centromere function by inhibiting deacetylases. Nat Cell Biol 3: 114-120.
56. Park PJ, (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
57. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
58. Karlić R, Chung HR, Lasserre J, Vlahovicek K, Vingron M, (2010) Histone modification levels are predictive for gene expression. Proc Natl Acad Sci 107: 2926-2931.
59. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
60. Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, et al. (2010) Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 142: 967-980.
61. Liu W, Tanasa B, Tyurina OV, Zhou TY, Gassmann R, et al. (2010) PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression. Nature 466: 508-512.
62. Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, et al. (2010) Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 466: 503-507.
63. Smit AFA, Hubley R, Green P (1996-2010). RepeatMasker Open-3.0. http://www.repeatmasker.org. URL http://www.repeatmasker.org.
64. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39: D876-D882.
65. Deal RB, Henikoff JG, Henikoff S, (2010) Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones. Science 328: 1161-1164.
66. Beisel C, Paro R, (2011) Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet 12: 123-135.
67. Duan Q, Chen H, Costa M, Dai W, (2008) Phosphorylation of H3S10 blocks the access of H3K9 by specific antibodies and histone methyltransferase. Implication in regulating chromatin dynamics and epigenetic inheritance during mitosis. J Biol Chem 283: 33585-33590.
68. Hatano A, Matsumoto M, Higashinakagawa T, Nakayama KI, (2010) Phosphorylation of the chromodomain changes the binding specificity of Cbx2 for methylated histone H3. Biochem Biophys Res Commun 397: 93-99.
69. Kang X, Qi Y, Zuo Y, Wang Q, Zou Y, et al. (2010) SUMO-specific protease 2 is essential for suppression of polycomb group protein-mediated gene silencing during embryonic development. Mol Cell 38: 191-201.
70. LeRoy G, Weston JT, Zee BM, Young NL, Plazas-Mayorca MD, et al. (2009) Heterochromatin protein 1 is extensively decorated with histone code-like post-translational modifications. Mol Cell Proteomics 8: 2432-2442.
71. Finelli P, Sirchia SM, Masciadri M, Crippa M, Recalcati MP, et al. (2012) Juxtaposition of heterochromatic and euchromatic regions by chromosomal translocation mediates a heterochromatic long-range position effect associated with a severe neurological phenotype. Mol Cytogenet 5: 16.
72. Sidoli S, Cheng L, Jensen ON, (2012) Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry. J Proteomics 75: 3419.
73. Xu H, Handoko L, Wei X, Ye C, Sheng J, et al. (2010) A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics 26: 1199-1204.
74. KentWJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.