Transcriptional Regulators Compete with Nucleosomes Post-replication

Cell

Volumn 165, Issue 3, 2016, Pages 580-592

  Ramachandran, Srinivas ^a,b   Henikoff, Steven ^a,b  

^a Fred Hutchinson Cancer Research Center   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYURIDINE DERIVATIVE; DNA; ETHYNYLDEOXYURIDINE; RNA POLYMERASE II; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; CHROMATIN; NUCLEOSOME;

ARTICLE; BINDING COMPETITION; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN REPLICATION; CHROMOSOMAL MAPPING; CHROMOSOME REPLICATION; CONTROLLED STUDY; DROSOPHILA; ENHANCER REGION; GENE SEQUENCE; IN VIVO STUDY; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION; ANIMAL; CELL CYCLE S PHASE; DNA REPLICATION; DROSOPHILA MELANOGASTER; GENETIC TRANSCRIPTION; METABOLISM;

ANIMALS; CHROMATIN; DNA REPLICATION; DROSOPHILA MELANOGASTER; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; RNA POLYMERASE II; S PHASE; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84962698776     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2016.02.062     Document Type: Article

References (50)

1. C. Alabert, T.K. Barth, N. Reverón-Gómez, S. Sidoli, A. Schmidt, O.N. Jensen, A. Imhof, and A. Groth Two distinct modes for propagation of histone PTMs across the cell cycle Genes Dev. 29 2015 585 590
2. A.E. Anderson, U.C. Karandikar, K.L. Pepple, Z. Chen, A. Bergmann, and G. Mardon The enhancer of trithorax and polycomb gene Caf1/p55 is essential for cell survival and patterning in Drosophila development Development 138 2011 1957 1966
3. A.T. Annunziato The fork in the road: histone partitioning during DNA replication Genes (Basel) 6 2015 353 371
4. J.A. Armstrong, O. Papoulas, G. Daubresse, A.S. Sperling, J.T. Lis, M.P. Scott, and J.W. Tamkun The Drosophila BRM complex facilitates global transcription by RNA polymerase II EMBO J. 21 2002 5245 5254
5. C.D. Arnold, D. Gerlach, C. Stelzer, L.M. Boryń, M. Rath, and A. Stark Genome-wide quantitative enhancer activity maps identified by STARR-seq Science 339 2013 1074 1077
6. M. Asano, and R.P. Wharton E2F mediates developmental and cell cycle regulation of ORC1 in Drosophila EMBO J. 18 1999 2435 2448
7. S.P. Bell, and A. Dutta DNA replication in eukaryotic cells Annu. Rev. Biochem. 71 2002 333 374
8. A.B. Blumenthal, H.J. Kriegstein, and D.S. Hogness The units of DNA replication in Drosophila melanogaster chromosomes Cold Spring Harb. Symp. Quant. Biol. 38 1974 205 223
9. B.R. Carone, J.H. Hung, S.J. Hainer, M.T. Chou, D.M. Carone, Z. Weng, T.G. Fazzio, and O.J. Rando High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm Dev. Cell 30 2014 11 22
10. K. Chen, Y. Xi, X. Pan, Z. Li, K. Kaestner, J. Tyler, S. Dent, X. He, and W. Li DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing Genome Res. 23 2013 341 351
11. M. Clemente-Ruiz, R. González-Prieto, and F. Prado Histone H3K56 acetylation, CAF1, and Rtt106 coordinate nucleosome assembly and stability of advancing replication forks PLoS Genet. 7 2011 e1002376
12. R. Dammann, R. Lucchini, T. Koller, and J.M. Sogo Chromatin structures and transcription of rDNA in yeast Saccharomyces cerevisiae Nucleic Acids Res. 21 1993 2331 2338
13. R.B. Deal, J.G. Henikoff, and S. Henikoff Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones Science 328 2010 1161 1164
14. A. Groth, A. Corpet, A.J. Cook, D. Roche, J. Bartek, J. Lukas, and G. Almouzni Regulation of replication fork progression through histone supply and demand Science 318 2007 1928 1931
15. U. Günesdogan, H. Jäckle, and A. Herzig Histone supply regulates S phase timing and cell cycle progression eLife 3 2014 e02443
16. F.N. Hamada, P.J. Park, P.R. Gordadze, and M.I. Kuroda Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster Genes Dev. 19 2005 2289 2294
17. J.G. Henikoff, J.A. Belsky, K. Krassovsky, D.M. MacAlpine, and S. Henikoff Epigenome characterization at single base-pair resolution Proc. Natl. Acad. Sci. USA 108 2011 18318 18323
18. J.R. Hesselberth, X. Chen, Z. Zhang, P.J. Sabo, R. Sandstrom, A.P. Reynolds, R.E. Thurman, S. Neph, M.S. Kuehn, W.S. Noble, and et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting Nat. Methods 6 2009 283 289
19. M. Hoek, and B. Stillman Chromatin assembly factor 1 is essential and couples chromatin assembly to DNA replication in vivo Proc. Natl. Acad. Sci. USA 100 2003 12183 12188
20. P.D. Kaufman, and O.J. Rando Chromatin as a potential carrier of heritable information Curr. Opin. Cell Biol. 22 2010 284 290
21. A. Kaykov, and P. Nurse The spatial and temporal organization of origin firing during the S-phase of fission yeast Genome Res. 25 2015 391 401
22. P.V. Kharchenko, A.A. Alekseyenko, Y.B. Schwartz, A. Minoda, N.C. Riddle, J. Ernst, P.J. Sabo, E. Larschan, A.A. Gorchakov, T. Gu, and et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster Nature 471 2011 480 485
23. B. Klapholz, B.H. Dietrich, C. Schaffner, F. Hérédia, J.P. Quivy, G. Almouzni, and N. Dostatni CAF-1 is required for efficient replication of euchromatic DNA in Drosophila larval endocycling cells Chromosoma 118 2009 235 248
24. K.H. Leung, M. Abou El Hassan, and R. Bremner A rapid and efficient method to purify proteins at replication forks under native conditions Biotechniques 55 2013 204 206
25. Y. Lorch, J.W. LaPointe, and R.D. Kornberg Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones Cell 49 1987 203 210
26. Y. Lubelsky, J.A. Prinz, L. DeNapoli, Y. Li, J.A. Belsky, and D.M. MacAlpine DNA replication and transcription programs respond to the same chromatin cues Genome Res. 24 2014 1102 1114
27. R. Lucchini, R.E. Wellinger, and J.M. Sogo Nucleosome positioning at the replication fork EMBO J. 20 2001 7294 7302
28. D.M. MacAlpine, and G. Almouzni Chromatin and DNA replication Cold Spring Harb. Perspect. Biol. 5 2013 a010207
29. H.K. MacAlpine, R. Gordân, S.K. Powell, A.J. Hartemink, and D.M. MacAlpine Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading Genome Res. 20 2010 201 211
30. S.L. McKnight, and O.L. Miller Jr. Electron microscopic analysis of chromatin replication in the cellular blastoderm Drosophila melanogaster embryo Cell 12 1977 795 804
31. Y.M. Moshkin, J.A. Armstrong, R.K. Maeda, J.W. Tamkun, P. Verrijzer, J.A. Kennison, and F. Karch Histone chaperone ASF1 cooperates with the Brahma chromatin-remodelling machinery Genes Dev. 16 2002 2621 2626
32. Y.M. Moshkin, G.E. Chalkley, T.W. Kan, B.A. Reddy, Z. Ozgur, W.F. van Ijcken, D.H. Dekkers, J.A. Demmers, A.A. Travers, and C.P. Verrijzer Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner Mol. Cell. Biol. 32 2012 675 688
33. S. Nakano, B. Stillman, and H.R. Horvitz Replication-coupled chromatin assembly generates a neuronal bilateral asymmetry in C. elegans Cell 147 2011 1525 1536
34. G.J. Narlikar, R. Sundaramoorthy, and T. Owen-Hughes Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes Cell 154 2013 490 503
35. G.A. Orsi, S. Kasinathan, K.T. Hughes, S. Saminadin-Peter, S. Henikoff, and K. Ahmad High-resolution mapping defines the cooperative architecture of Polycomb response elements Genome Res. 24 2014 809 820
36. F. Prado, F. Cortés-Ledesma, and A. Aguilera The absence of the yeast chromatin assembly factor Asf1 increases genomic instability and sister chromatid exchange EMBO Rep. 5 2004 497 502
37. S. Ramachandran, and S. Henikoff Replicating nucleosomes Sci Adv 1 2015 e1500587
38. A. Rizzino, and A.B. Blumenthal Synchronization of Drosophila cells in culture In Vitro 14 1978 437 442
39. A. Salic, and T.J. Mitchison A chemical method for fast and sensitive detection of DNA synthesis in vivo Proc. Natl. Acad. Sci. USA 105 2008 2415 2420
40. B.M. Sirbu, F.B. Couch, J.T. Feigerle, S. Bhaskara, S.W. Hiebert, and D. Cortez Analysis of protein dynamics at active, stalled, and collapsed replication forks Genes Dev. 25 2011 1320 1327
41. B.M. Sirbu, F.B. Couch, and D. Cortez Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA Nat. Protoc. 7 2012 594 605
42. P.J. Skene, and S. Henikoff A simple method for generating high-resolution maps of genome-wide protein binding eLife 4 2015 e09225
43. S.S. Teves, and S. Henikoff Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide Genes Dev. 25 2011 2387 2397
44. T. Tsukiyama, P.B. Becker, and C. Wu ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor Nature 367 1994 525 532
45. C.M. Weber, J.G. Henikoff, and S. Henikoff H2A.Z nucleosomes enriched over active genes are homotypic Nat. Struct. Mol. Biol. 17 2010 1500 1507
46. C.M. Weber, S. Ramachandran, and S. Henikoff Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase Mol. Cell 53 2014 819 830
47. A. Weiner, A. Hughes, M. Yassour, O.J. Rando, and N. Friedman High-resolution nucleosome mapping reveals transcription-dependent promoter packaging Genome Res. 20 2010 90 100
48. I. Whitehouse, and D.J. Smith Chromatin dynamics at the replication fork: there's more to life than histones Curr. Opin. Genet. Dev. 23 2013 140 146
49. J.O. Yáñez-Cuna, C.D. Arnold, G. Stampfel, L.M. Boryń, D. Gerlach, M. Rath, and A. Stark Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features Genome Res. 24 2014 1147 1156
50. G.C. Yuan, Y.J. Liu, M.F. Dion, M.D. Slack, L.F. Wu, S.J. Altschuler, and O.J. Rando Genome-scale identification of nucleosome positions in S. cerevisiae Science 309 2005 626 630