Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

Genome Research

Volumn 23, Issue 7, 2013, Pages 1142-1154

  Ernst, Jason ^a,b   Kellis, Manolis ^c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE;

ARTICLE; CELL TYPE; CHROMATIN; CONTROLLED STUDY; FEMALE; GENE SEQUENCE; HISTONE MODIFICATION; HUMAN; HUMAN CELL; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION;

BINDING SITES; CELL LINE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CLUSTER ANALYSIS; ENHANCER ELEMENTS, GENETIC; HUMANS; NUCLEOTIDE MOTIFS; ORGAN SPECIFICITY; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS;

EID: 84880064679     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.144840.112     Document Type: Article

References (61)

1. Applegate DL, Bixby RE, Chvatal V, Cook WJ. 2006. The traveling salesman problem: A computational study. Princeton University Press, Princeton, NJ.
2. Bar-Joseph Z, Gifford DK, Jaakkola TS. 2001. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics 17: S22.
3. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE,Wang Z,Wei G, Chepelev I, Zhao K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
4. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, et al. 2006. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.
5. Biedl T, Brejová B, Demaine ED, Hamel AM, Vinar T. 2001. Optimal arrangement of leaves in the tree representing hierarchical clustering of gene expression data. Tech. Rep. 2001, Department of Computer Science, University of Waterloo, Ontario, Canada, p. 14.
6. Blank V. 2008. Small Maf proteins in mammalian gene control: Mere dimerization partners or dynamic transcriptional regulators? J Mol Biol 376: 913-925.
7. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. 2008. High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311-322.
8. Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, et al. 2012. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390-394.
9. The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
10. Ernst J, Kellis M. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
11. Ernst J, KellisM. 2012.ChromHMM: Automating chromatin-state discovery and characterization. Nat Methods 9: 215-216.
12. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
13. Essien K, Vigneau S, Apreleva S, Singh LN, Bartolomei MS, Hannenhalli S. 2009. CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features. Genome Biol 10: R131.
14. Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M. 2011. Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet 7: e1002008.
15. Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ. 2010. ZNF274 recruits the histone methyltransferase SETDB1 to the 39 ends of ZNF genes. PLoS ONE 5: e15082.
16. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, et al. 2012. Architecture of the human regulatory network derived from ENCODE data. Nature 489: 91-100.
17. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104.
18. Heintzman ND, Stuart RK, Hon G, Fu Y, ChingCW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, et al. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311-318.
19. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW, et al. 2009. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108-112.
20. Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, KuehnMS, Noble WS, et al. 2009. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods 6: 283-289.
21. Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, et al. 2013. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res 41: 827-841.
22. Hon G, Ren B, Wang W. 2008. ChromaSig: A probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol 4: e1000201.
23. Jaschek R, Tanay A. 2009. Spatial clustering of multivariate genomic and epigenomic information. In Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2009, pp. 170-183. Springer-Verlag, Berlin.
24. John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. 2011. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 43: 264-268.
25. Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB. 2011. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet 7: e1001290.
26. Kharchenko PV, Tolstorukov MY, Park PJ. 2008. Design and analysis of ChIPseq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
27. Kheradpour P, Stark A, Roy S, KellisM. 2007. Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res 17: 1919-1931.
28. Lam FH, Steger DJ, O'Shea EK. 2008. Chromatin decouples promoter threshold from dynamic range. Nature 453: 246-250.
29. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, et al. 2012. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22: 1813-1831.
30. Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D, Zhuo D, Stoeckert CJ Jr, Liu XS, et al. 2008. PPARg and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 22: 2941-2952.
31. Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL, et al. 2008. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27.
32. Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD. 2011. The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol 12: R34.
33. Lickwar CR,Mueller F, Hanlon SE, McNally JG, Lieb JD. 2012. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484: 251-255.
34. LupienM, Eeckhoute J, Meyer CA,WangQ, Zhang Y, LiW, Carroll JS, Liu XS, Brown M. 2008. FoxA1 translates epigenetic signatures into enhancerdriven lineage-specific transcription. Cell 132: 958-970.
35. Meissner A. 2010. Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol 28: 1079-1088.
36. The modENCODE Consortium. 2010. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-1797.
37. Montgomery SB, Sammeth M, Gutierrez-ArcelusM, Lach RP, Ingle C,Nisbett J, Guigo R, Dermitzakis ET. 2010. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
38. Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, et al. 2006. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proc Natl Acad Sci 103: 12027-12032.
39. Mullen AC, Orlando DA, Newman JJ, Loven J, Kumar RM, Bilodeau S, Reddy J, Guenther MG, DeKoter RP, Young RA. 2011. Master transcription factors determine cell-type-specific responses to TGF-b signaling. Cell 147: 565-576.
40. Negre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, et al. 2011. A cis-regulatory map of the Drosophila genome. Nature 471: 527-531.
41. Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C. 2008. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res 18: 380.
42. Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, et al. 2008. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res 18: 1906-1917.
43. Sanyal A, Lajoie BR, Jain G, Dekker J. 2012. The long-range interaction landscape of gene promoters. Nature 489: 109-113.
44. Schultz DC, Ayyanathan K, Negorev D, Maul GG, Rauscher FJ III. 2002. SETDB1: A novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev 16: 919-932.
45. Segal E,Widom J. 2009. From DNA sequence to transcriptional behaviour: A quantitative approach. Nat Rev Genet 10: 443-456.
46. Siersbaek R, Nielsen R, John S, Sung MH, Baek S, Loft A, Hager GL, Mandrup S. 2011. Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis. EMBO J 30: 1459-1472.
47. Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, HussM, Keefe D, et al. 2011. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res 21: 1757-1767.
48. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, et al. 2011. The BioGRID interaction database: 2011 update. Nucleic Acids Res 39: D698-D704.
49. Steger DJ, Grant GR, Schupp M, Tomaru T, Lefterova MI, Schug J, Manduchi E, Stoeckert CJ Jr, Lazar MA. 2010. Propagation of adipogenic signals through an epigenomic transition state. Genes Dev 24: 1035-1044.
50. Takahashi K, Yamanaka S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663-676.
51. Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA. 2007. Identification of higher-order functional domains in the human ENCODE regions. Genome Res 17: 917-927.
52. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, et al. 2012. The accessible chromatin landscape of the human genome. Nature 489: 75-82.
53. Trompouki E, Bowman TV, Lawton LN, Fan ZP, Wu DC, DiBiase A, Martin CS, Cech JN, Sessa AK, Leblanc JL, et al. 2011. Lineage regulators direct BMP and Wnt pathways to cell-specific programs during differentiation and regeneration. Cell 147: 577-589.
54. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, et al. 2009. ChIP-seq accurately predicts tissuespecific activity of enhancers. Nature 457: 854-858.
55. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, et al. 2008. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
56. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, et al. 2012. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 22: 1798-1812.
57. Wendt KS, Peters JM. 2009. How cohesin and CTCF cooperate in regulating gene expression. Chromosome Res 17: 201-214.
58. Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, et al. 2011. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res 21: 1659-1671.
59. Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS, et al. 2007. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet 3: e136.
60. Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, et al. 2012. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol 13: R48.
61. Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, et al. 2010. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet 6: e1000848.