Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Genome Research

Volumn 22, Issue 9, 2012, Pages 1798-1812

  Wang, Jie ^a   Zhuang, Jiali ^a   Iyer, Sowmya ^a,b   Lin, XinYing ^a   Whitfield, Troy W ^a   Greven, Melissa C ^a   Pierce, Brian G ^a   Dong, Xianjun ^a   Kundaje, Anshul ^c   Cheng, Yong ^d   Rando, Oliver J ^a   Birney, Ewan ^e   Myers, Richard M ^f   Noble, William S ^g   Snyder, Michael ^d   Weng, Zhiping ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b BOSTON UNIVERSITY   (United States)

^c Stanford University   (United States)

^d STANFORD UNIVERSITY   (United States)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^f HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^g UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CCAAT ENHANCER BINDING PROTEIN EP300; COHESIN; DEOXYRIBONUCLEASE I; HEAT SHOCK PROTEIN; HISTONE DEACETYLASE 2; NUCLEIC ACID BINDING PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CELL TYPE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; DNA BINDING MOTIF; DNA FOOTPRINTING; GENE EXPRESSION; GENE SEQUENCE; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; NUCLEOSOME; PRIORITY JOURNAL;

BASE COMPOSITION; BINDING SITES; CELL LINE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DEOXYRIBONUCLEASE I; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; NUCLEOSOMES; NUCLEOTIDE MOTIFS; ORGAN SPECIFICITY; PROTEIN BINDING; TRANSCRIPTION FACTORS;

EID: 84865852567     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.139105.112     Document Type: Article

References (65)

1. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, et al. 2009. Diversity and complexity in DNA recognition by transcription factors. Science 324: 1720-1723.
2. Berger SL. 2007. The complex language of chromatin regulation during transcription. Nature 447: 407-412. (Pubitemid 46816746)
3. Biggin MD. 2011. Animal transcription networks as highly connected, quantitative continua. Dev Cell 21: 611-626.
4. Bilodeau S, Kagey MH, Frampton GM, Rahl PB, Young RA. 2009. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev 23: 2484-2489.
5. Bourque G, Leong B, Vega VB, Chen X, Lee YL, Srinivasan KG, Chew J-L, Ruan Y, Wei C-L, Ng H-H, et al. 2008. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res 18: 1752-1762.
6. Boyd KE, Farnham PJ. 1997. Myc versus USF: Discrimination at the cad gene is determined by core promoter elements. Mol Cell Biol 17: 2529-2537. (Pubitemid 27175134)
7. Bryne JC, Valen E, Tang M-HE, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A. 2008. JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update. Nucleic Acids Res 36: D102-D106. (Pubitemid 351149704)
8. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, et al. 2006. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 38: 1289-1297. (Pubitemid 44646291)
9. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, et al. 2008. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 1106-1117. (Pubitemid 351787745)
10. Clapier CR, Cairns BR. 2009. The biology of chromatin remodeling complexes. Annu Rev Biochem 78: 273-304.
11. Cohen C, Rebollo R, Babovic S, Dai E, Robinson W, Mager D. 2011. Placenta-specific expression of the interleukin-2 (IL-2) receptor b subunit from an endogenous retroviral promoter. J Biol Chem 286: 35543-35552.
12. de Nigris F, Botti C, Rossiello R, Crimi E, Sica V, Napoli C. 2007. Cooperation between Myc and YY1 provides novel silencing transcriptional targets of α3β1-integrin in tumour cells. Oncogene 26: 382-394. (Pubitemid 46122828)
13. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi AM, Tanzer A, Lagarde J, Lin W, Schlesinger F, et al. 2012. Landscape of transcription in human cells. Nature (in press).
14. The ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9: e1001046. doi: 10.1371/journal.pbio. 1001046.
15. Felsenfeld G. 1996. Chromatin unfolds. Cell 86: 13-19. (Pubitemid 26256574)
16. Frietze S, O'Geen H, Blahnik K, Jin VX, Farnham PJ. 2010. ZNF274 recruits the histone methyltransferase SETDB1 to the 3′ ends of ZNF genes. PLoS ONE 5: e15082. doi: 10.1371/journal.pone.0015082.
17. Fu Y, Sinha M, Peterson CL, Weng Z. 2008. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet 4: e1000138. doi: 10.1371/journal.pgen.1000138.
18. Guertin MJ, Lis JT. 2010. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet 6: e1001114. doi: 10.1371/journal.pgen.1001114.
19. Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. 2007. Quantifying similarity between motifs. Genome Biol 8: R24. doi: 10.1186/gb-2007-8-2-r24.
20. He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, et al. 2010. Nucleosome dynamics define transcriptional enhancers. Nat Genet 42: 343-347.
21. Hu X, Li X, Valverde K, Fu X, Noguchi C, Qiu Y, Huang S. 2009. LSD1-mediated epigenetic modification is required for TAL1 function and hematopoiesis. Proc Natl Acad Sci 106: 10141-10146.
22. Huang Y, Myers SJ, Dingledine R. 1999. Transcriptional repression by REST: Recruitment of Sin3A and histone deacetylase to neuronal genes. Nat Neurosci 2: 867-872. (Pubitemid 30602598)
23. John S, Sabo PJ, Thurman RE, Sung M-H, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. 2011. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 43: 264-268.
24. Kardassis D, Falvey E, Tsantili P, Hadzopoulou-Cladaras M, Zannis V. 2002. Direct physical interactions between HNF-4 and Sp1 mediate synergistic transactivation of the apolipoprotein CIII promoter. Biochemistry 41: 1217-1228. (Pubitemid 34083774)
25. Kashyap V, Rezende NC, Scotland KB, Shaffer SM, Persson JL, Gudas LJ, Mongan NP. 2009. Regulation of stem cell pluripotency and differentiation involves a mutual regulatory circuit of the NANOG, OCT4, and SOX2 pluripotency transcription factors with polycomb repressive complexes and stem cell microRNAs. Stem Cells Dev 18: 1093-1108.
26. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. Circos: An information aesthetic for comparative genomics. Genome Res 19: 1639-1645.
27. Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. 2012. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res (this issue). doi: 10.1101/gr.136366.111.
28. Lemaigre F, Zaret KS. 2004. Liver development update: New embryo models, cell lineage control, and morphogenesis. Curr Opin Genet Dev 14: 582-590. (Pubitemid 39360307)
29. Levine M, Tjian R. 2003. Transcription regulation and animal diversity. Nature 424: 147-151. (Pubitemid 36858677)
30. Li X-Y, 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. doi: 10.1186/gb-2011-12-4-r34.
31. Machanick P, Bailey TL. 2011. MEME-ChIP: Motif analysis of large DNA datasets. Bioinformatics 27: 1696-1697.
32. MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ. 2011. Genome-wide transcription factor binding: Beyond direct target regulation. Trends Genet 27: 141-148.
33. Maston GA, Evans SK, Green MR. 2006. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 7: 29-59. (Pubitemid 44627921)
34. Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, et al. 2003. TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31: 374-378. (Pubitemid 36150406)
35. Mink S, Haenig B, Klempnauer KH. 1997. Interaction and functional collaboration of p300 and C/EBPb. Mol Cell Biol 17: 6609-6617. (Pubitemid 27451207)
36. Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. 2010. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol 17: 635-640.
37. Myslinski E, Gérard M-A, Krol A, Carbon P. 2006. A genome scale location analysis of human Staf/ZNF143-binding sites suggests a widespread role for human Staf/ZNF143 in mammalian promoters. J Biol Chem 281: 39953-39962. (Pubitemid 46041799)
38. Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, Sandstrom R, Johnson AK, Maurano MT, et al. 2012. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature (in press).
39. Oettel S, Kober I, Seifart KH. 1998. The activity binding to the termination region of several pol III genes represents a separate entity and is distinct from a novel component enhancing U6 snRNA transcription. Nucleic Acids Res 26: 4324-4331. (Pubitemid 28442121)
40. Ohlsson R, Renkawitz R, Lobanenkov V. 2001. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet 17: 520-527. (Pubitemid 32763050)
41. Parelho V, Hadjur S, Spivakov M, Leleu M, Sauer S, Gregson HC, Jarmuz A, Canzonetta C, Webster Z, Nesterova T, et al. 2008. Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132: 422-433.
42. Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. 2007. Nucleosome positioning signals in genomic DNA. Genome Res 17: 1170-1177. (Pubitemid 47204860)
43. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. 2010. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20: 110-121.
44. Radman-Livaja M, Rando OJ. 2010. Nucleosome positioning: How is it established, and why does it matter? Dev Biol 339: 258-266.
45. Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, et al. 2010. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140: 744-752.
46. Rhee HS, Pugh BF. 2011. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147: 1408-1419.
47. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657. (Pubitemid 47202477)
48. Roder K, Wolf SS, Larkin KJ, Schweizer M. 1999. Interaction between the two ubiquitously expressed transcription factors NF-Y and Sp1. Gene 234: 61-69. (Pubitemid 29291645)
49. Runkel L, Shaw PE, Herrera RE, Hipskind RA, Nordheim A. 1991. Multiple basal promoter elements determine the level of human c-fos transcription. Mol Cell Biol 11: 1270-1280. (Pubitemid 21895483)
50. Sabogal A, Lyubimov AY, Corn JE, Berger JM, Rio DC. 2010. THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Nat Struct Mol Biol 17: 117-123.
51. Sawadogo M, Luo X, Sirito M, Lu T. 1999. Biological function of the USF family of transcription factors. Gene Ther Mol Biol 3: 447-453.
52. Schmid C, Bucher P. 2010. MER41 repeat sequences contain inducible STAT1 binding sites. PLoS ONE 5: e11425. doi: 10.1371/journal.pone.0011425.
53. Sokalski KM, Li SKH, Welch I, Cadieux-Pitre H-AT, Gruca MR, DeKoter RP. 2011. Deletion of genes encoding PU.1 and Spi-B in B cells impairs differentiation and induces pre-B cell acute lymphoblastic leukemia. Blood 118: 2801-2808.
54. Stark C, Breitkreutz B-J, Reguly T, Boucher L, Breitkreutz A, Tyers M. 2006. BioGRID: A general repository for interaction datasets. Nucleic Acids Res 34: D535-D539.
55. Takahashi S, Onodera K, Motohashi H, Suwabe N, Hayashi N, Yanai N, Nabesima Y, Yamamoto M. 1997. Arrest in primitive erythroid cell development caused by promoter-specific disruption of the GATA-1 gene. J Biol Chem 272: 12611-12615. (Pubitemid 27203356)
56. Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. 2011. Determinants of nucleosome organization in primary human cells. Nature 474: 516-520.
57. Wang C, Rauscher FJ, Cress WD, Chen J. 2007. Regulation of E2F1 function by the nuclear corepressor KAP1. J Biol Chem 282: 29902-29909. (Pubitemid 350035243)
58. Wang C-C, Tsai M-F, Dai T-H, Hong T-M, Chan W-K, Chen JJW, Yang P-C. 2007. Synergistic activation of the tumor suppressor, HLJ1, by the transcription factors YY1 and activator protein 1. Cancer Res 67: 4816-4826. (Pubitemid 46910190)
59. Wang Y-L, Faiola F, Xu M, Pan S, Martinez E. 2008. Human ATAC Is a GCN5/ PCAF-containing acetylase complex with a novel NC2-like histone fold module that interacts with the TATA-binding protein. J Biol Chem 283: 33808-33815.
60. Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N. 2010. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res 20: 90-100.
61. Weintraub H, Groudine M. 1976. Chromosomal subunits in active genes have an altered conformation. Science 193: 848-856.
62. Whitfield TW, Wang J, Collins PJ, Partridge EC, Trinklein ND, Aldred SF, Myers RM, Weng Z. 2012. Functional analysis of transcription factor binding sites in human promoters. Genome Biol (in press).
63. Xu Z, Huang S, Chang L-S, Agulnick AD, Brandt SJ. 2003. Identification of a TAL1 target gene reveals a positive role for the LIM domain-binding protein Ldb1 in erythroid gene expression and differentiation. Mol Cell Biol 23: 7585-7599. (Pubitemid 37271458)
64. Yoon H-G, Chan DW, Reynolds AB, Qin J, Wong J. 2003. N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso. Mol Cell 12: 723-734. (Pubitemid 37222492)
65. Zhou Z, Li X, Deng C, Ney PA, Huang S, Bungert J. 2010. USF and NF-E2 cooperate to regulate the recruitment and activity of RNA polymerase II in the β-globin gene locus. J Biol Chem 285: 15894-15905.