Generation of bivalent chromatin domains during cell fate decisions

Epigenetics and Chromatin

Volumn 4, Issue 1, 2011, Pages

  De Gobbi, Marco ^a   Garrick, David ^a   Lynch, Magnus ^a   Vernimmen, Douglas ^a   Hughes, Jim R ^a   Goardon, Nicolas ^a   Luc, Sidinh ^a   Lower, Karen M ^a   Sloane Stanley, Jacqueline A ^a   Pina, Cristina ^a   Soneji, Shamit ^a   Renella, Raffaele ^a   Enver, Tariq ^a   Taylor, Stephen ^b   Jacobsen, Sten Eirik W ^a   Vyas, Paresh ^a,b   Gibbons, Richard J ^a   Higgs, Douglas R ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA GLOBIN; HISTONE H3;

CELL DIFFERENTIATION; CELL FATE; CELL LINEAGE; CHROMATIN; CHROMOSOME 16P; CONTROLLED STUDY; EPIGENETICS; ERYTHROID CELL; GENE EXPRESSION; GENE LOCUS; HEMATOPOIETIC STEM CELL; HISTONE MODIFICATION; HUMAN; HUMAN CELL; PRIORITY JOURNAL; REVIEW; TELOMERE;

EID: 79957926708     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-4-9     Document Type: Review

References (38)

1. Chromatin signatures of pluripotent cell lines. V Azuara P Perry S Sauer M Spivakov HF Jorgensen RM John M Gouti M Casanova G Warnes M Merkenschlager AG Fisher, Nat Cell Biol 2006 8 532 538 10.1038/ncb1403 16570078
2. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. BE Bernstein TS Mikkelsen X Xie M Kamal DJ Huebert J Cuff B Fry A Meissner M Wernig K Plath R Jaenisch A Wagschal R Feil SL Schreiber ES Lander, Cell 2006 125 315 326 10.1016/j.cell.2006.02.041 16630819
3. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. TS Mikkelsen M Ku DB Jaffe B Issac E Lieberman G Giannoukos P Alvarez W Brockman TK Kim RP Koche W Lee E Mendenhall A O'Donovan A Presser C Russ X Xie A Meissner M Wernig R Jaenisch C Nusbaum ES Lander BE Bernstein, Nature 2007 448 553 560 10.1038/nature06008 17603471 (Pubitemid 47206934)
4. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. G Pan S Tian J Nie C Yang V Ruotti H Wei GA Jonsdottir R Stewart JA Thomson, Cell Stem Cell 2007 1 299 312 10.1016/j.stem.2007.08.003 18371364 (Pubitemid 47355329)
5. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. XD Zhao X Han JL Chew J Liu KP Chiu A Choo YL Orlov WK Sung A Shahab VA Kuznetsov G Bourque S Oh Y Ruan HH Ng CL Wei, Cell Stem Cell 2007 1 286 298 10.1016/j.stem.2007.08.004 18371363 (Pubitemid 47370914)
6. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. M Ku RP Koche E Rheinbay EM Mendenhall M Endoh TS Mikkelsen A Presser C Nusbaum X Xie AS Chi M Adli S Kasif LM Ptaszek CA Cowan ES Lander H Koseki BE Bernstein, PLoS Genet 2008 4 1000242 10.1371/journal.pgen.1000242 18974828
7. Stem cell regulation by polycomb repressors: postponing commitment. AM Pietersen M van Lohuizen, Curr Opin Cell Biol 2008 20 201 207 10.1016/j.ceb.2008.01.004 18291635
8. A chromatin landmark and transcription initiation at most promoters in human cells. MG Guenther SS Levine LA Boyer R Jaenisch RA Young, Cell 2007 130 77 88 10.1016/j.cell.2007.05.042 17632057 (Pubitemid 47031323)
9. Modifications of RNA polymerase II are pivotal in regulating gene expression states. E Brookes A Pombo, EMBO Rep 2009 10 1213 1219 10.1038/embor.2009.221 19834511
10. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. A Kanhere K Viiri CC Araujo J Rasaiyaah RD Bouwman WA Whyte CF Pereira E Brookes K Walker GW Bell A Pombo AG Fisher RA Young RG Jenner, Mol Cell 2010 38 675 688 10.1016/j.molcel.2010.03.019 20542000
11. Polycomb complexes repress developmental regulators in murine embryonic stem cells. LA Boyer K Plath J Zeitlinger T Brambrink LA Medeiros TI Lee SS Levine M Wernig A Tajonar MK Ray GW Bell AP Otte M Vidal DK Gifford RA Young R Jaenisch, Nature 2006 441 349 353 10.1038/nature04733 16625203 (Pubitemid 44050199)
12. Polycomb repressive complex 2 is dispensable for maintenance of embryonic stem cell pluripotency. SJ Chamberlain D Yee T Magnuson, Stem Cells 2008 26 1496 1505 10.1634/stemcells.2008-0102 18403752
13. Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. H Jiang A Skukla X Wang WY Chen BE Bernstein RG Roeder, Cell 2011 144 513 525 10.1016/j.cell.2011.01.020 21335234
14. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. YS Ang SY Tsai DF Lee J Monk J Su K Ratnakumar J Ding Y Ge H Darr B Chang J Wang M Rendl E Bernstein C Schaniel IR Leminschka, Cell 2011 145 183 197 10.1016/j.cell.2011.03.003 21477851
15. Global transcription in pluripotent embryonic stem cells. S Efroni R Duttagupta J Cheng H Dehghani DJ Hoeppner C Dash DP Bazett-Jones S Le Grice RD McKay KH Buetow TR Gingeras T Misteli E Meshorer, Cell Stem Cell 2008 2 437 447 10.1016/j.stem.2008.03.021 18462694 (Pubitemid 351598083)
16. The genomic landscape of histone modifications in human T cells. TY Roh S Cuddapah K Cui K Zhao, Proc Natl Acad Sci USA 2006 103 15782 15787 10.1073/pnas.0607617103 17043231 (Pubitemid 44657544)
17. High-resolution profiling of histone methylations in the human genome. A Barski S Cuddapah K Cui TY Roh DE Schones Z Wang G Wei I Chepelev K Zhao, Cell 2007 129 823 837 10.1016/j.cell.2007.05.009 17512414 (Pubitemid 46802390)
18. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. K Cui C Zang TY Roh DE Schones RW Childs W Peng K Zhao, Cell Stem Cell 2009 4 80 93 10.1016/j.stem.2008.11.011 19128795
19. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. M Adli J Zhu BE Bernstein, Nat Methods 7 615 618
20. Epigenetic control of embryonic stem cell fate. NS Christophersen K Helin, J Exp Med 207 2287 95
21. Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. JR Hughes JF Cheng N Ventress S Prabhakar K Clark E Anguita M De Gobbi P de Jong E Rubin DR Higgs, Proc Natl Acad Sci USA 2005 102 9830 9835 10.1073/pnas.0503401102 15998734 (Pubitemid 40993653)
22. Chromosome looping at the human alpha-globin locus is mediated via the major upstream regulatory element (HS-40). D Vernimmen F Marques-Kranc JA Sharpe JA Sloane-Stanley WG Wood HA Wallace AJ Smith DR Higgs, Blood 2009 114 4253 4260 10.1182/blood-2009-03-213439 19696202
23. Non-methylated CpG-rich islands at the human alpha-globin locus: implications for evolution of the alpha-globin pseudogene. AP Bird MH Taggart RD Nicholls DR Higgs, EMBO J 1987 6 999 1004 3595568
24. Globin gene activation during haemopoiesis is driven by protein complexes nucleated by GATA-1 and GATA-2. E Anguita J Hughes C Heyworth GA Blobel WG Wood DR Higgs, EMBO J 2004 23 2841 2852 10.1038/sj.emboj.7600274 15215894 (Pubitemid 39013556)
25. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. D Vernimmen M De Gobbi JA Sloane-Stanley WG Wood DR Higgs, EMBO J 2007 26 2041 2051 10.1038/sj.emboj. 7601654 17380126 (Pubitemid 46625789)
26. Tissue-specific histone modification and transcription factor binding in alpha globin gene expression. M De Gobbi E Anguita J Hughes JA Sloane-Stanley JA Sharpe CM Koch I Dunham RJ Gibbons WG Wood DR Higgs, Blood 2007 110 4503 4510 10.1182/blood-2007-06-097964 17715390 (Pubitemid 351377817)
27. The role of the polycomb complex in silencing alpha-globin gene expression in nonerythroid cells. D Garrick M De Gobbi V Samara M Rugless M Holland H Ayyub K Lower J Sloane-Stanley N Gray C Koch I Dunham DR Higgs, Blood 2008 112 3889 3899 10.1182/blood-2008-06-161901 18689541
28. A newly discovered human -globin gene. SH Goh Y Terry Lee NV Bhanu MC Cam R Desper BM Martin R Moharram RB Gherman JL Miller, Blood 2005 106 1466 1472 10.1182/blood-2005-03-0948 15855277 (Pubitemid 41129617)
29. Single-cell transcript analysis of human embryonic stem cells. JD Gibson CM Jakuba N Boucher KA Holbrook MG Carter CE Nelson, Integr Biol (Camb) 2009 1 540 551 10.1039/b908276j
30. A signaling mechanism for growth-related expression of fetal hemoglobin. NV Bhanu TA Trice YT Lee JL Miller, Blood 2004 103 1929 1933 10.1182/blood-2003-05-1624 14592835 (Pubitemid 38268993)
31. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. D Schubeler DM MacAlpine D Scalzo C Wirbelauer C Kooperberg F van Leeuwen DE Gottschling LP O'Neill BM Turner J Delrow SP Bell M Groudine, Genes Dev 2004 18 1263 1271 10.1101/gad.1198204 15175259 (Pubitemid 38720594)
32. Epigenetic chromatin states uniquely define the developmental plasticity of murine hematopoietic stem cells. H Weishaupt M Sigvardsson JL Attema, Blood 2010 115 247 256 10.1182/blood-2009-07-235176 19887676
33. Multilineage gene expression precedes commitment in the hemopoietic system. M Hu D Krause M Greaves S Sharkis M Dexter C Heyworth T Enver, Genes Dev 1997 11 774 785 10.1101/gad.11.6.774 9087431 (Pubitemid 27157165)
34. Control of stochasticity in eukatyotic gene expression. JM Rase EK O'Shea, Science 2004 304 1811 1814 10.1126/science.1098641 15166317 (Pubitemid 38787899)
35. Two-phase liquid culture system models normal human adult erythropoiesis at the molecular level. SH Pope E Fibach J Sun K Chin GP Rodgers, Eur J Haematol 2000 64 292 303 10.1034/j.1600-0609.2000.90032.x 10863975 (Pubitemid 30307701)
36. Coregulated human globin genes are frequently in spatial proximity when active. JM Brown J Leach JE Reittie A Atzberger J Lee-Prudhoe WG Wood DR Higgs FJ Iborra VJ Buckle, J Cell Biol 2006 172 177 187 10.1083/jcb.200507073 16418531 (Pubitemid 43112966)
37. Molecular evidence for hierarchical transcriptional lineage priming in fetal and adult stem cells and multipotent progenitors. R Mansson A Hultquist S Luc L Yang K Anderson S Kharazi S Al-Hashmi K Liuba L Thoren J Adolfsson N Buza-Vidas H Qian S Soneji T Enver M Sigvardsson SE Jacobsen, Immunity 2007 26 407 419 10.1016/j.immuni.2007.02.013 17433729 (Pubitemid 46603001)
38. Profile of histone lysine methylation across transcribed mammalian chromatin. CR Vakoc MM Sachdeva H Wang GA Blobel, Mol Cel Biol 2006 26 9185 9195 10.1128/MCB.01529-06 (Pubitemid 44904415)