Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains

Epigenetics and Chromatin

Volumn 6, Issue 1, 2013, Pages

  Takebayashi, Shin Ichiro ^a   Lei, Ienglam ^b,c,d   Ryba, Tyrone ^a   Sasaki, Takayo ^a   Dileep, Vishnu ^a   Battaglia, Dana ^a   Gao, Xiaolin ^b,c   Fang, Peng ^b,c   Fan, Yong ^b,c   Esteban, Miguel A ^e   Tang, Jiong ^f   Crabtree, Gerald R ^f   Wang, Zhong ^b,c,d   Gilbert, David M ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

^b MASSACHUSETTS GENERAL HOSPITAL   (United States)

^c HARVARD STEM CELL INSTITUTE   (United States)

^d UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^e INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^f STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Chromosome; Developmental regulation; esBAF complex; Replication domains; Replication timing

Indexed keywords

BAF250A PROTEIN; BRG1 PROTEIN; DNA; PROTEIN; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; DNA REPLICATION TIMING; EMBRYO; FIBROBLAST; MOUSE; NONHUMAN; NUCLEAR REPROGRAMMING; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; PROTEIN BINDING;

MURINAE;

EID: 84889993685     PISSN: None     EISSN: 17568935     Source Type: Journal    
DOI: 10.1186/1756-8935-6-42     Document Type: Article

References (44)

1. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Bantignies F, Roure V, Comet I, Leblanc B, Schuettengruber B, Bonnet J, Tixier V, Mas A, Cavalli G, Cell 2011 144 214 226 10.1016/j.cell.2010.12.026 21241892
2. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Hakim O, Sung MH, Voss TC, Splinter E, John S, Sabo PJ, Thurman RE, Stamatoyannopoulos JA, de Laat W, Hager GL, Genome Res 2011 21 697 706 10.1101/gr.111153.110 21471403
3. A regulatory archipelago controls Hox genes transcription in digits. Montavon T, Soshnikova N, Mascrez B, Joye E, Thevenet L, Splinter E, de Laat W, Spitz F, Duboule D, Cell 2011 147 1132 1145 10.1016/j.cell.2011.10.023 22118467
4. Three-dimensional folding and functional organization principles of the Drosophila genome. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G, Cell 2012 148 458 472 10.1016/j.cell.2012.01.010 22265598
5. Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding. Takebayashi S, Dileep V, Ryba T, Dennis JH, Gilbert DM, Proc Natl Acad Sci USA 2012 109 12574 12579 10.1073/pnas.1207185109 22807480
6. Global reorganization of replication domains during embryonic stem cell differentiation. Hiratani I, Ryba T, Itoh M, Yokochi T, Schwaiger M, Chang CW, Lyou Y, Townes TM, Schubeler D, Gilbert DM, PLoS Biol 2008 6 245 10.1371/journal.pbio.0060245 18842067
7. Genome-scale analysis of replication timing: from bench to bioinformatics. Ryba T, Battaglia D, Pope BD, Hiratani I, Gilbert DM, Nat Protoc 2011 6 870 895 10.1038/nprot.2011.328 21637205
8. Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Hiratani I, Ryba T, Itoh M, Rathjen J, Kulik M, Papp B, Fussner E, Bazett-Jones DP, Plath K, Dalton S, Rathjen PD, Gilbert DM, Genome Res 2010 20 155 169 10.1101/gr.099796.109 19952138
9. Abnormal developmental control of replication timing domains in pediatric acute lymphoblastic leukemia. Ryba T, Battaglia D, Chang BH, Shirley JW, Buckley Q, Pope BD, Devidas M, Druker BJ, Gilbert DM, Genome Res 2012 22 1833 1844 10.1101/gr.138511.112 22628462
10. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Schulz TC, Robins AJ, Dalton S, Gilbert DM, Genome Res 2010 20 761 770 10.1101/gr.099655.109 20430782
11. Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. Yaffe E, Farkash-Amar S, Polten A, Yakhini Z, Tanay A, Simon I, PLoS Genet 2010 6 1001011 10.1371/journal.pgen.1001011 20617169
12. Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Pope BD, Chandra T, Buckley Q, Hoare M, Ryba T, Wiseman FK, Kuta A, Wilson MD, Odom DT, Gilbert DM, Hum Mol Genet 2012 21 4162 4170 10.1093/hmg/dds232 22736031
13. Uncoupling global and fine-tuning replication timing determinants for mouse pericentric heterochromatin. Wu R, Singh PB, Gilbert DM, J Cell Biol 2006 174 185 194 10.1083/jcb.200601113 16831888
14. The impact of chromatin modifiers on the timing of locus replication in mouse embryonic stem cells. Jorgensen HF, Azuara V, Amoils S, Spivakov M, Terry A, Nesterova T, Cobb BS, Ramsahoye B, Merkenschlager M, Fisher AG, Genome Biol 2007 8 169 10.1186/gb-2007-8-8-r169 17705870
15. G9a selectively represses a class of late-replicating genes at the nuclear periphery. Yokochi T, Poduch K, Ryba T, Lu J, Hiratani I, Tachibana M, Shinkai Y, Gilbert DM, Proc Natl Acad Sci USA 2009 106 19363 19368 10.1073/pnas.0906142106 19889976
16. Forkhead transcription factors establish origin timing and long-range clustering in S. cerevisiae. Knott SR, Peace JM, Ostrow AZ, Gan Y, Rex AE, Viggiani CJ, Tavare S, Aparicio OM, Cell 2012 148 99 111 10.1016/j.cell.2011.12. 012 22265405
17. Rif1 is a global regulator of timing of replication origin firing in fission yeast. Hayano M, Kanoh Y, Matsumoto S, Renard-Guillet C, Shirahige K, Masai H, Genes Dev 2012 26 137 150 10.1101/gad.178491.111 22279046
18. Mouse Rif1 is a key regulator of the replication-timing programme in mammalian cells. Cornacchia D, Dileep V, Quivy JP, Foti R, Tili F, Santarella-Mellwig R, Antony C, Almouzni G, Gilbert DM, Buonomo SB, EMBO J 2012 31 3678 3690 10.1038/emboj.2012.214 22850673
19. Rif1 regulates the replication timing domains on the human genome. Yamazaki S, Ishii A, Kanoh Y, Oda M, Nishito Y, Masai H, EMBO J 2012 31 3667 3677 10.1038/emboj.2012.180 22850674
20. The chromatin remodeling complex NoRC controls replication timing of rRNA genes. Li J, Santoro R, Koberna K, Grummt I, EMBO J 2005 24 120 127 10.1038/sj.emboj.7600492 15577942
21. BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Yan Z, Wang Z, Sharova L, Sharov AA, Ling C, Piao Y, Aiba K, Matoba R, Wang W, Ko MS, Stem Cells 2008 26 1155 1165 10.1634/stemcells.2007-0846 18323406
22. Understanding the words of chromatin regulation. Wu JI, Lessard J, Crabtree GR, Cell 2009 136 200 206 10.1016/j.cell.2009.01.009 19167321
23. MicroRNA-mediated switching of chromatin-remodelling complexes in neural development. Yoo AS, Staahl BT, Chen L, Crabtree GR, Nature 2009 460 642 646 19561591
24. Chromatin remodelling during development. Ho L, Crabtree GR, Nature 2010 463 474 484 10.1038/nature08911 20110991
25. The ground state of embryonic stem cell self-renewal. Ying QL, Wray J, Nichols J, Batlle-Morera L, Doble B, Woodgett J, Cohen P, Smith A, Nature 2008 453 519 523 10.1038/nature06968 18497825
26. Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming. Singhal N, Graumann J, Wu G, Arauzo-Bravo MJ, Han DW, Greber B, Gentile L, Mann M, Scholer HR, Cell 2010 141 943 955 10.1016/j.cell.2010.04.037 20550931
27. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Lessard J, Wu JI, Ranish JA, Wan M, Winslow MM, Staahl BT, Wu H, Aebersold R, Graef IA, Crabtree GR, Neuron 2007 55 201 215 10.1016/j.neuron.2007.06.019 17640523
28. MicroRNA-mediated conversion of human fibroblasts to neurons. Yoo AS, Sun AX, Li L, Shcheglovitov A, Portmann T, Li Y, Lee-Messer C, Dolmetsch RE, Tsien RW, Crabtree GR, Nature 2011 476 228 231 10.1038/nature10323 21753754
29. Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors. Takeuchi JK, Bruneau BG, Nature 2009 459 708 711 10.1038/nature08039 19396158
30. ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a. Gao X, Tate P, Hu P, Tjian R, Skarnes WC, Wang Z, Proc Natl Acad Sci USA 2008 105 6656 6661 10.1073/pnas.0801802105 18448678
31. ARID1a-DNA interactions are required for promoter occupancy by SWI/SNF. Chandler RL, Brennan J, Schisler JC, Serber D, Patterson C, Magnuson T, Mol Cell Biol 2013 33 265 280 10.1128/MCB.01008-12 23129809
32. An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Ho L, Ronan JL, Wu J, Staahl BT, Chen L, Kuo A, Lessard J, Nesvizhskii AI, Ranish J, Crabtree GR, Proc Natl Acad Sci USA 2009 106 5181 5186 10.1073/pnas.0812889106 19279220
33. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Ho L, Miller EL, Ronan JL, Ho WQ, Jothi R, Crabtree GR, Nat Cell Biol 2011 13 903 913 10.1038/ncb2285 21785422
34. The BAF53a subunit of SWI/SNF-like BAF complexes is essential for hemopoietic stem cell function. Krasteva V, Buscarlet M, Diaz-Tellez A, Bernard MA, Crabtree GR, Lessard JA, Blood 2012 120 4720 4732 10.1182/blood-2012-04- 427047 23018638
35. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Ho L, Jothi R, Ronan JL, Cui K, Zhao K, Crabtree GR, Proc Natl Acad Sci USA 2009 106 5187 5191 10.1073/pnas.0812888106 19279218
36. Replication timing and transcriptional control: beyond cause and effect-part II. Hiratani I, Takebayashi S, Lu J, Gilbert DM, Curr Opin Genet Dev 2009 19 142 149 10.1016/j.gde.2009.02.002 19345088
37. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J, Science 2009 326 289 293 10.1126/science.1181369 19815776
38. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B, Nature 2012 485 376 380 10.1038/nature11082 22495300
39. BRG1 requirement for long-range interaction of a locus control region with a downstream promoter. Kim SI, Bultman SJ, Kiefer CM, Dean A, Bresnick EH, Proc Natl Acad Sci USA 2009 106 2259 2264 10.1073/pnas.0806420106 19171905
40. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Takahashi K, Yamanaka S, Cell 2006 126 663 676 10.1016/j.cell.2006.07.024 16904174
41. SWI/SNF component BAF250a regulates cardiac progenitor cell differentiation by modulating chromatin accessibility during second heart field development. Lei I, Gao X, Sham MH, Wang Z, J Biol Chem 2012 287 24255 24262 10.1074/jbc.M112.365080 22621927
42. Purification and biochemical heterogeneity of the mammalian SWI-SNF complex. Wang W, Cote J, Xue Y, Zhou S, Khavari PA, Biggar SR, Muchardt C, Kalpana GV, Goff SP, Yaniv M, Workman JL, Crabtree GR, EMBO J 1996 15 5370 5382 8895581
43. Visualization of transcription-dependent association of imprinted genes with the nuclear matrix. Kagotani K, Nabeshima H, Kohda A, Nakao M, Taguchi H, Okumura K, Exp Cell Res 2002 274 189 196 10.1006/excr.2002.5478 11900479
44. ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data. Weddington N, Stuy A, Hiratani I, Ryba T, Yokochi T, Gilbert DM, BMC Bioinforma 2008 9 530 10.1186/1471-2105-9-530