Dynamic changes of the epigenetic landscape during cellular differentiation

Epigenomics

Volumn 5, Issue 6, 2013, Pages 701-713

  Dambacher, Silvia ^a   De Almeida, Gustavo Pereira ^a   Schotta, Gunnar ^a  

^a Munich Center for Integrated Protein Science   (Germany)

Author keywords

differentiation; DNA methylation; histone modification; lineage commitment; lineage decision; reprogramming; stem cell

Indexed keywords

POLYCOMB GROUP PROTEIN; TRANSCRIPTION FACTOR;

CELL DIFFERENTIATION; CHROMATIN; DNA METHYLATION; EPIGENETICS; GENE ACTIVATION; GENE REPRESSION; GENE SILENCING; HETEROCHROMATIN; HISTONE MODIFICATION; HUMAN; NONHUMAN; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; REGENERATIVE MEDICINE; REVIEW;

CELL DIFFERENTIATION; CHROMATIN; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION; HISTONES; HUMANS; ORGAN SPECIFICITY; PLURIPOTENT STEM CELLS; TRANSCRIPTION FACTORS;

EID: 84889651853     PISSN: 17501911     EISSN: 1750192X     Source Type: Journal    
DOI: 10.2217/epi.13.67     Document Type: Review

References (99)

1. Heintzman ND, Stuart RK, Hon G et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39(3), 311-318 (2007
2. Ku M, Jaffe JD, Koche RP et al. H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biol. 13(10), R85 (2012
3. Ghisletti S, Barozzi I, Mietton F et al. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32(3), 317-328 (2010
4. Heintzman ND, Hon GC, Hawkins RD et al. Histone modifications at human enhancers reflect global cell-Type-specific gene expression. Nature 459(7243), 108-112 (2009
5. Heinz S, Benner C, Spann N et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38(4), 576-589 (2010
6. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470(7333), 279-283 (2011
7. Visel A, Blow MJ, Li Z et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457(7231), 854-858 (2009
8. Creyghton MP, Cheng AW, Welstead GG et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107(50), 21931-21936 (2010
9. Guenther MG, Levine SS, Boyer LA, Jaenisch R, Young RA. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130(1), 77-88 (2007
10. Mikkelsen TS, Ku M, Jaffe DB et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153), 553-560 (2007
11. Shilatifard A. The COMPASS family of histone H3K4 methylases: Mechanisms of regulation in development and disease pathogenesis. Annu. Rev. Biochem. 81, 65-95 (2012
12. Vermeulen M, Mulder KW, Denissov S et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131(1), 58-69 (2007
13. Moriniere J, Rousseaux S, Steuerwald U et al. Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature 461(7264), 664-668 (2009
14. Jacobson RH, Ladurner AG, King DS, Tjian R. Structure and function of a human TAFII250 double bromodomain module. Science 288(5470), 1422-1425 (2000
15. Lauberth SM, Nakayama T, Wu X et al. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell 152(5), 1021-1036 (2013
16. Hodl M, Basler K. Transcription in the absence of histone H3.2 and H3K4 methylation. Curr. Biol. 22(23), 2253-2257 (2012
17. Jin C, Felsenfeld G. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev. 21(12), 1519-1529 (2007
18. Hu G, Cui K, Northrup D et al. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell 12(2), 180-192 (2013
19. Clouaire T, Webb S, Skene P et al. Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells. Genes Dev. 26(15), 1714-1728 (2012
20. Thomson JP, Skene PJ, Selfridge J et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464(7291), 1082-1086 (2010
21. Long HK, Blackledge NP, Klose RJ. ZF-CXXC domain-containing proteins, CpG islands and the chromatin connection. Biochem. Soc. Trans. 41(3), 727-740 (2013
22. Conaway RC, Conaway JW. The mediator complex and transcription elongation. Biochim. Biophys. Acta 1829(1), 69-75 (2013
23. Luo Z, Lin C, Shilatifard A. The super elongation complex (SEC) family in transcriptional control. Nat. Rev. Mol. Cell Biol. 13(9), 543-547 (2012
24. Palermo RD, Webb HM, West MJ. RNA polymerase II stalling promotes nucleosome occlusion and pTEFb recruitment to drive immortalization by Epstein-Barr virus. PLoS Pathog. 7(10), e1002334 (2011
25. Rahman S, Sowa ME, Ottinger M et al. The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3. Mol. Cell. Biol. 31(13), 2641-2652 (2011
26. Yoh SM, Lucas JS, Jones KA. The Iws1:Spt6:CTD complex controls cotranscriptional mRNA biosynthesis and HYPB/Setd2-mediated histone H3K36 methylation. Genes Dev. 22(24), 3422-3434 (2008
27. Carvalho S, Raposo AC, Martins FB et al. Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription. Nucleic Acids Res. 41(5), 2881-2893 (2013
28. Margueron R, Li G, Sarma K et al. Ezh1 and Ezh2 maintain repressive chromatin through different mechanisms. Mol. Cell 32(4), 503-518 (2008
29. Shen X, Liu Y, Hsu YJ et al. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol. Cell 32(4), 491-502 (2008
30. Gao Z, Zhang J, Bonasio R et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol. Cell 45(3), 344-356 (2012
31. Zhou W, Zhu P, Wang J et al. Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation. Mol. Cell 29(1), 69-80 (2008
32. Eskeland R, Leeb M, Grimes GR et al. Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol. Cell 38(3), 452-464 (2010
33. Grau DJ, Chapman BA, Garlick JD, Borowsky M, Francis NJ, Kingston RE. Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge. Genes Dev. 25(20), 2210-2221 (2011
34. Kaustov L, Ouyang H, Amaya M et al. Recognition and specificity determinants of the human CBX chromodomains. J. Biol. Chem. 286(1), 521-529 (2011
35. Farcas AM, Blackledge NP, Sudbery I et al. KDM2B links the Polycomb repressive complex 1 (PRC1) to recognition of CpG islands. Elife 1, e00205 (2012
36. He J, Shen L, Wan M, Taranova O, Wu H, Zhang Y. Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. Nat. Cell Biol. 15(4), 373-384 (2013
37. Wu X, Johansen JV, Helin K. Fbxl10/Kdm2b recruits Polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Mol. Cell 49(6), 1134-1146 (2013
38. Arnold P, Scholer A, Pachkov M et al. Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome Res. 23(1), 60-73 (2013
39. Cabianca DS, Casa V, Bodega B et al. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149(4), 819-831 (2012
40. Rinn JL, Kertesz M, Wang JK et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7), 1311-1323 (2007
41. Bernstein BE, Mikkelsen TS, Xie X et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125(2), 315-326 (2006
42. Voigt P, Leroy G, Drury WJ 3rd et al. Asymmetrically modified nucleosomes. Cell 151(1), 181-193 (2012
43. Stock JK, Giadrossi S, Casanova M et al. Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells. Nat. Cell Biol. 9(12), 1428-1435 (2007
44. Min IM, Waterfall JJ, Core LJ, Munroe RJ, Schimenti J, Lis JT. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. Genes Dev. 25(7), 742-754 (2011
45. Schotta G, Lachner M, Sarma K et al. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 18(11), 1251-1262 (2004
46. Schotta G, Sengupta R, Kubicek S et al. A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse. Genes Dev. 22(15), 2048-2061 (2008
47. Hahn M, Dambacher S, Dulev S et al. Suv4-20h2 mediates chromatin compaction and is important for cohesin recruitment to heterochromatin. Genes Dev. 27(8), 859-872 (2013
48. Allan RS, Zueva E, Cammas F et al. An epigenetic silencing pathway controlling T helper 2 cell lineage commitment. Nature 487(7406), 249-253 (2012
49. Bilodeau S, Kagey MH, Frampton GM, Rahl PB, Young RA. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev. 23(21), 2484-2489 (2009
50. Yuan P, Han J, Guo G et al. Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells. Genes Dev. 23(21), 2507-2520 (2009
51. Karimi MM, Goyal P, Maksakova IA et al. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 8(6), 676-687 (2011
52. Hawkins RD, Hon GC, Lee LK et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6(5), 479-491 (2010
53. Tan SL, Nishi M, Ohtsuka T et al. Essential roles of the histone methyltransferase ESET in the epigenetic control of neural progenitor cells during development. Development 139(20), 3806-3816 (2012
54. Liu X, Gao Q, Li P et al. UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9. Nat. Commun. 4, 1563 (2013
55. Stadler MB, Murr R, Burger L et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480(7378), 490-495 (2011
56. Williams K, Christensen J, Helin K DNA methylation: TET proteins-guardians of CpG islands? EMBO Rep. 13(1), 28-35 (2012
57. Nan X, Ng HH, Johnson CA et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393(6683), 386-389 (1998
58. Baubec T, Ivanek R, Lienert F, Schubeler D. Methylation-dependent and-independent genomic targeting principles of the MBD protein family. Cell 153(2), 480-492 (2013
59. Lehnertz B, Ueda Y, Derijck AA et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13(14), 1192-1200 (2003
60. Arand J, Spieler D, Karius T et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 8(6), e1002750 (2012
61. Li H, Rauch T, Chen ZX, Szabo PE, Riggs AD, Pfeifer GP. The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells. J. Biol. Chem. 281(28), 19489-19500 (2006
62. Quenneville S, Turelli P, Bojkowska K et al. The KRAB-ZFP/KAP1 system contributes to the early embryonic establishment of site-specific DNA methylation patterns maintained during development. Cell Rep. 2(4), 766-773 (2012
63. Brinkman AB, Gu H, Bartels SJ et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-Talk. Genome Res. 22(6), 1128-1138 (2012
64. Hagarman JA, Motley MP, Kristjansdottir K, Soloway PD. Coordinate regulation of DNA methylation and H3K27me3 in mouse embryonic stem cells. PLoS ONE 8(1), e53880 (2013
65. Schlesinger Y, Straussman R, Keshet I et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet. 39(2), 232-236 (2007
66. Wu H, Coskun V, Tao J et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329(5990), 444-448 (2010
67. Hodges E, Smith AD, Kendall J et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res. 19(9), 1593-1605 (2009
68. Dhayalan A, Rajavelu A, Rathert P et al. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J. Biol. Chem. 285(34), 26114-26120 (2010
69. Hahn MA, Wu X, Li AX, Hahn T, Pfeifer GP. Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks. PLoS ONE 6(4), e18844 (2011
70. Zhu J, Adli M, Zou JY et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152(3), 642-654 (2013
71. Lieberman-Aiden E, Van Berkum NL, Williams L et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326(5950), 289-293 (2009
72. Guelen L, Pagie L, Brasset E et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453(7197), 948-951 (2008
73. Meissner A, Mikkelsen TS, Gu H et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454(7205), 766-770 (2008
74. Mohn F, Weber M, Rebhan M et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol. Cell 30(6), 755-766 (2008
75. Bock C, Beerman I, Lien WH et al. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol. Cell 47(4), 633-647 (2012
76. Ernst J, Kheradpour P, Mikkelsen TS et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473(7345), 43-49 (2011
77. Gifford CA, Ziller MJ, Gu H et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell 153(5), 1149-1163 (2013
78. Xie W, Schultz MD, Lister R et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153(5), 1134-1148 (2013
79. Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res. 21(8), 1273-1283 (2011
80. Wamstad JA, Alexander JM, Truty RM et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell 151(1), 206-220 (2012
81. Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell 149(2), 467-482 (2012
82. Li Z, Gadue P, Chen K et al. Foxa2 and H2A.Z mediate nucleosome depletion during embryonic stem cell differentiation. Cell 151(7), 1608-1616 (2012
83. Tan L, Shi YG. Tet family proteins and 5-hydroxymethylcytosine in development and disease. Development 139(11), 1895-1902 (2012
84. Kooistra SM, Helin K. Molecular mechanisms and potential functions of histone demethylases. Nat. Rev. Mol. Cell Biol. 13(5), 297-311 (2012
85. Chen X, Xu H, Yuan P et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133(6), 1106-1117 (2008
86. Aksoy I, Jauch R, Chen J et al. Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO J. 32(7), 938-953 (2013
87. Whyte WA, Bilodeau S, Orlando DA et al. Enhancer decommissioning by LSD1 during embryonic stem cell differentiation. Nature 482(7384), 221-225 (2012
88. Lassar AB, Paterson BM, Weintraub H. Transfection of a DNA locus that mediates the conversion of 10T1/2 fibroblasts to myoblasts. Cell 47(5), 649-656 (1986
89. Ladewig J, Koch P, Brustle O. Leveling Waddington: The emergence of direct programming and the loss of cell fate hierarchies. Nat. Rev. Mol. Cell Biol. 14(4), 225-236 (2013
90. Huangfu D, Maehr R, Guo W et al. Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat. Biotechnol. 26(7), 795-797 (2008
91. Mikkelsen TS, Hanna J, Zhang X et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454(7200), 49-55 (2008
92. Onder TT, Kara N, Cherry A et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature 483(7391), 598-602 (2012
93. Ruiz S, Diep D, Gore A et al. Identification of a specific reprogramming-Associated epigenetic signature in human induced pluripotent stem cells. Proc. Natl Acad. Sci. USA 109(40), 16196-16201 (2012
94. Soufi A, Donahue G, Zaret KS. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151(5), 994-1004 (2012
95. Chen J, Liu H, Liu J et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat. Genet. 45(1), 34-42 (2013
96. You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang G, Jones PA. OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes. Proc. Natl Acad. Sci. USA 108(35), 14497-14502 (2011
97. Gifford CA, Meissner A. Epigenetic obstacles encountered by transcription factors: Reprogramming against all odds. Curr. Opin. Genet. Dev. 22(5), 409-415 (2012
98. Gaj T, Gersbach CA, Barbas CF 3rd. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 31(7), 397-405 (2013
99. Bae JB. Perspectives of international human epigenome consortium. Genomics Inform. 11(1), 7-14 (2013