Switching between Epigenetic States at Pericentromeric Heterochromatin

Trends in Genetics

Volumn 31, Issue 11, 2015, Pages 661-672

  Déjardin, Jérôme ^a  

^a INSTITUTE OF HUMAN GENETICS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HETEROCHROMATIN PROTEIN 1; HISTONE H3; LYSINE; POLYCOMB GROUP PROTEIN; TRANSCRIPTION FACTOR; DNA (CYTOSINE 5) METHYLTRANSFERASE; HETEROCHROMATIN; HISTONE; PAIRED BOX TRANSCRIPTION FACTOR;

BIOGENESIS; CANCER CELL; CANCER TISSUE; COMPLEX FORMATION; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION; HETEROCHROMATIN; HISTONE METHYLATION; HUMAN; MOLECULAR BIOLOGY; NONHUMAN; PERICENTROMERIC HETEROCHROMATIN; PRIORITY JOURNAL; REVIEW; TRANSCRIPTION REGULATION; TRIMETHYLATION; ANIMAL; CENTROMERE; GENETIC EPIGENESIS; GENETICS; METABOLISM; MOUSE; SIGNAL TRANSDUCTION; ULTRASTRUCTURE;

ANIMALS; CENTROMERE; DNA; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA METHYLATION; EPIGENESIS, GENETIC; HETEROCHROMATIN; HISTONES; HUMANS; MICE; PAIRED BOX TRANSCRIPTION FACTORS; POLYCOMB-GROUP PROTEINS; SIGNAL TRANSDUCTION;

EID: 84946198627     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2015.09.003     Document Type: Review

References (76)

1. Trojer P., Reinberg D. Facultative heterochromatin: is there a distinctive molecular signature?. Mol. Cell 2007, 28:1-13.
2. Mikkelsen T.S., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
3. Filion G.J., et al. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 2010, 143:212-224.
4. Matsuda Y., Chapman V.M. In situ analysis of centromeric satellite DNA segregating in Mus species crosses. Mamm. Genome 1991, 1:71-77.
5. Zhang X.Y., Horz W. Nucleosomes are positioned on mouse satellite DNA in multiple highly specific frames that are correlated with a diverged subrepeat of nine base-pairs. J. Mol. Biol. 1984, 176:105-129.
6. Peters A.H., et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 2001, 107:323-337.
7. Wang H., et al. mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression. Mol. Cell 2003, 12:475-487.
8. Loyola A., et al. The HP1alpha-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin. EMBO Rep. 2009, 10:769-775.
9. Sanchez R., Zhou M.M. The PHD finger: a versatile epigenome reader. Trends Biochem. Sci. 2011, 36:364-372.
10. Eissenberg J.C. Structural biology of the chromodomain: form and function. Gene 2012, 496:69-78.
11. Lu R., Wang G.G. Tudor: a versatile family of histone methylation 'readers'. Trends Biochem. Sci. 2013, 38:546-555.
12. Muramatsu D., et al. Pericentric heterochromatin generated by HP1 protein interaction-defective histone methyltransferase Suv39h1. J. Biol. Chem. 2013, 288:25285-25296.
13. Bulut-Karslioglu A., et al. A transcription factor-based mechanism for mouse heterochromatin formation. Nat. Struct. Mol. Biol. 2012, 19:1023-1030.
14. Bostick M., et al. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 2007, 317:1760-1764.
15. Schultz M.D., et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 2015, 523:212-216.
16. Arand J., et al. Selective impairment of methylation maintenance is the major cause of DNA methylation reprogramming in the early embryo. Epigenetics Chromatin 2015, 8:1.
17. Probst A.V., et al. A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development. Dev. Cell 2010, 19:625-638.
18. Santenard A., et al. Heterochromatin formation in the mouse embryo requires critical residues of the histone variant H3.3. Nat. Cell Biol. 2010, 12:853-862.
19. Drew H.R., McCall M.J. Structural analysis of a reconstituted DNA containing three histone octamers and histone H5. J. Mol. Biol. 1987, 197:485-511.
20. Nightingale K., Wolffe A.P. Methylation at CpG sequences does not influence histone H1 binding to a nucleosome including a Xenopus borealis 5S rRNA gene. J. Biol. Chem. 1995, 270:4197-4200.
21. Collings C.K., et al. Effects of DNA methylation on nucleosome stability. Nucleic Acids Res. 2013, 41:2918-2931.
22. Georgel P.T., et al. Chromatin compaction by human MeCP2. Assembly of novel secondary chromatin structures in the absence of DNA methylation. J. Biol. Chem. 2003, 278:32181-32188.
23. Nikitina T., et al. MeCP2-chromatin interactions include the formation of chromatosome-like structures and are altered in mutations causing Rett syndrome. J. Biol. Chem. 2007, 282:28237-28245.
24. Walton E.L., et al. Dnmt3b prefers germ line genes and centromeric regions: lessons from the ICF syndrome and cancer and implications for diseases. Biol. (Basel) 2014, 3:578-605.
25. Lehnertz B., et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 2003, 13:1192-1200.
26. Smith Z.D., Meissner A. DNA methylation: roles in mammalian development. Nat. Rev. Genet. 2013, 14:204-220.
27. Arand J., et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 2012, 8:e1002750.
28. Okano M., et al. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999, 99:247-257.
29. Liu X., et al. UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9. Nat. Commun. 2013, 4:1563.
30. Saksouk N., et al. Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation. Mol. Cell 2014, 56:580-594.
31. Morselli M., et al. In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. Elife 2015, 4:e06205.
32. Noh K.M., et al. Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape and phenotypic features of mouse ESCs. Mol. Cell 2015, 59:89-103.
33. Tariq M., et al. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:8823-8827.
34. Tsumura A., et al. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 2006, 11:805-814.
35. Murphy P.J., et al. Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:7772-7777.
36. Jiang Y., et al. Setdb1-mediated histone H3K9 hypermethylation in neurons worsens the neurological phenotype of Mecp2-deficient mice. Neuropharmacology 2011, 60:1088-1097.
37. Cooper S., et al. Targeting polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment. Cell Rep. 2014, 7:1456-1470.
38. Simon J.A., Kingston R.E. Occupying chromatin: polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol. Cell 2013, 49:808-824.
39. Pengelly A.R., et al. A histone mutant reproduces the phenotype caused by loss of histone-modifying factor Polycomb. Science 2013, 339:698-699.
40. Kalb R., et al. Histone H2A monoubiquitination promotes histone H3 methylation in Polycomb repression. Nat. Struct. Mol. Biol. 2014, 21:569-571.
41. Blackledge N.P., et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell 2014, 157:1445-1459.
42. Boyer L.A., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006, 441:349-353.
43. Pasini D., et al. The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol. Cell. Biol. 2007, 27:3769-3779.
44. Ku M., et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 2008, 4:e1000242.
45. Dietrich N., et al. REST-mediated recruitment of polycomb repressor complexes in mammalian cells. PLoS Genet. 2012, 8:e1002494.
46. Brinkman A.B., et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012, 22:1128-1138.
47. Puschendorf M., et al. PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Nat. Genet. 2008, 40:411-420.
48. de Napoles M., et al. Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation. Dev. Cell 2004, 7:663-676.
49. Arney K.L., et al. Histone methylation defines epigenetic asymmetry in the mouse zygote. Int. J. Dev. Biol. 2002, 46:317-320.
50. Santos F., et al. Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. Dev. Biol. 2005, 280:225-236.
51. Abhiman S., et al. BEN: a novel domain in chromatin factors and DNA viral proteins. Bioinformatics 2008, 24:458-461.
52. Bartke T., et al. Nucleosome-interacting proteins regulated by DNA and histone methylation. Cell 2010, 143:470-484.
53. Iurlaro M., et al. A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation. Genome Biol. 2013, 14:R119.
54. Reynolds N., et al. NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression. EMBO J. 2012, 31:593-605.
55. Yuan W., et al. Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation. Science 2012, 337:971-975.
56. Brockdorff N. Noncoding RNA and Polycomb recruitment. RNA 2013, 19:429-442.
57. Davidovich C., et al. Toward a consensus on the binding specificity and promiscuity of PRC2 for RNA. Mol. Cell 2015, 57:552-558.
58. Bolden A., et al. DNA methylation. Inhibition of de novo and maintenance methylation in vitro by RNA and synthetic polynucleotides. J. Biol. Chem. 1984, 259:12437-12443.
59. Di Ruscio A., et al. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature 2013, 503:371-376.
60. Engreitz J.M., et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 2013, 341:1237973.
61. Simon M.D., et al. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 2013, 504:465-469.
62. Tardat M., et al. Cbx2 targets PRC1 to constitutive heterochromatin in mouse zygotes in a parent-of-origin-dependent manner. Mol. Cell 2015, 58:157-171.
63. Farcas A.M., et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife 2012, 1:e00205.
64. He J., et al. Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. Nat. Cell Biol. 2013, 15:373-384.
65. Saurin A.J., et al. The human polycomb group complex associates with pericentromeric heterochromatin to form a novel nuclear domain. J. Cell Biol. 1998, 142:887-898.
66. Martens J.H., et al. The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J. 2005, 24:800-812.
67. Eymery A., et al. A transcriptomic analysis of human centromeric and pericentric sequences in normal and tumor cells. Nucleic Acids Res. 2009, 37:6340-6354.
68. Ting D.T., et al. Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 2011, 331:593-596.
69. Zhu Q., et al. BRCA1 tumour suppression occurs via heterochromatin-mediated silencing. Nature 2011, 477:179-184.
70. Grewal S.I., Jia S. Heterochromatin revisited. Nat. Rev. Genet. 2007, 8:35-46.
71. Brown K.E., et al. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 1997, 91:845-854.
72. Dorer D.R., Henikoff S. Expansions of transgene repeats cause heterochromatin formation and gene silencing in Drosophila. Cell 1994, 77:993-1002.
73. Brower-Toland B., et al. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes Dev. 2007, 21:2300-2311.
74. Garrick D., et al. Repeat-induced gene silencing in mammals. Nat. Genet. 1998, 18:56-59.
75. Saveliev A., et al. DNA triplet repeats mediate heterochromatin-protein-1-sensitive variegated gene silencing. Nature 2003, 422:909-913.
76. Schmiedeberg L., et al. A temporal threshold for formaldehyde crosslinking and fixation. PLoS ONE 2009, 4:e4636.