Cell-type and transcription factor specific enrichment of transcriptional cofactor motifs in ENCODE ChIP-seq data

BMC Genomics

Volumn 14, Issue , 2013, Pages

  Goi, Chin Lui ^a,c   Little, Peter ^a,b,c   Xie, Chao ^b,c  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

HEPATOCYTE NUCLEAR FACTOR 4ALPHA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MYC PROTEIN; PLAGL1 PROTEIN; PROTEIN EBF1; REGULATOR PROTEIN; STAT3 PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 1; UNCLASSIFIED DRUG; DNA;

ARTICLE; BINDING SITE; CELL CULTURE; CELLS BY BODY ANATOMY; CELLULAR DISTRIBUTION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DATA ANALYSIS; DNA BINDING MOTIF; DNA SEQUENCE; HEP-G2 CELL LINE; IN VIVO STUDY; PHENOTYPE; PROTEIN INTERACTION; SEQUENCE ANALYSIS; CHEMISTRY; CHROMATIN; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; HELA CELL LINE; HEPG2 CELL LINE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CHROMOSOME; K562 CELL LINE; METABOLISM; METHODOLOGY; PROTEIN MOTIF;

AMINO ACID MOTIFS; BINDING SITES; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOMES, HUMAN; DNA; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HELA CELLS; HEP G2 CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; K562 CELLS; PHENOTYPE; TRANSCRIPTION FACTORS;

EID: 84908173072     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-S5-S2     Document Type: Article

References (55)

1. MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ: Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet 2011, 27(4):141-148
2. Sridharan R, Tchieu J, Mason MJ, Yachechko R, Kuoy E, Horvath S, Zhou Q, Plath K: Role of the murine reprogramming factors in the induction of pluripo-tency. Cell 2009, 136:364-377
3. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM: A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009, 10:252-263
4. Dang CV, O'Donnell KA, Zeller KI, Nguyen T, Osthus RC, Li F: The c-Myc target gene network. Semin Cancer Biol 2006, 16:253-264
5. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4:651-657
6. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simo-nis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabasi AL, Tavernier J, Hill DE, Vidal M: High-quality binary protein interaction map of the yeast interactome network. Science 2008, 322(5898):104-110
7. Park D, Lee S, Bolser D, Schroeder M, Lappe M, Oh D, Bhak J: Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map). Bioinformatics 2005, 21(15):3234-3240
8. Fields S, Song O: A novel genetic system to detect protein-protein interactions. Nature 1989, 340(6230):245-246
9. Parrish JR, Gulyas KD, Finley RL: Yeast two-hybrid contributions to interactome mapping. Curr Opin Biotechnol 2006, 17(4):387-393
10. Koegl M, Uetz P: Improving yeast two-hybrid screening systems. Brief Funct Genomic Proteomic 2007, 6:302-312
11. Pepke S, Wold B, Mortazavi A: Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6:22-32
12. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, Volkert TL, Wilson CJ, Bell SP, Young RA: Genome-wide location and function of DNA binding proteins. Science 2000, 290(5500):2306-2309
13. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409(6819):533-538
14. Farnham PJ: Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10:605-616
15. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A: Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 2008, 5:829-834
16. Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR: Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res 2012, 22:9-24
17. ENCODE Project Consortium: The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640
18. Whitington T, Frith MC, Johnson J, Bailey TL: Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Res 2011, 39(15):e98
19. van Steensel B: Chromatin: constructing the big picture. EMBO J 2011, 30:1885-1895
20. Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B: Hotspots of transcription factor colocal-ization in the genome of Drosophila melanogaster. Proc Natl Acad Sci USA 2006, 103:12027-12032
21. Negre N, Brown CD, Ma L, Bristow CA, Miller SW, Wag-ner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R, Li Z, Ishii H, Spokony RF, Chen J, Hwang L, Cheng C, Auburn RP, Davis MB, Domanus M, Shah PK, Mor-rison CA, Zieba J, Suchy S, Senderowicz L, Victorsen A, Bild NA, Grundstad AJ, Hanley D, MacAlpine DM, Mannervik M, Venken K, Bellen H, White R, Gerstein M, Russell S, Grossman RL, Ren B, Posakony JW, Kellis M, White KP: A cisregulatory map of the Drosophila genome. Nature 2011, 471:527-531
22. Ellrott K, Yang C, Sladek FM, Jiang T: Identifying transcription factor binding sites through Markov chain optimization. Bioinformatics 2002, 18(Suppl 2):S100-109
23. Duda K, Chi YI, Shoelson SE: Structural basis for HNF-4alpha activation by ligand and coactivator binding. J Biol Chem 2004, 279:23311-23316
24. Zhang X, Wrzeszczynska MH, Horvath CM, Darnell JE: Interacting regions in Stat3 and c-Jun that participate in cooperative transcriptional activation. Mol Cell Biol 1999, 19(10):7138-7146
25. Ito T, Tanahashi H, Misumi Y, Sakaki Y: Nuclear factors interacting with an interleukin-6 responsive element of rat alpha 2-macroglobulin gene. Nucleic Acids Res 1989, 17(22):9425-9435
26. Leu JI, Crissey MA, Leu JP, Ciliberto G, Taub R: Interleukin-6-induced STAT3 and AP-1 amplify hepatocyte nuclear factor 1-mediated transactivation of hepatic genes, an adaptive response to liver injury. Mol Cell Biol 2001, 21(2):414-424
27. Schaefer TS, Sanders LK, Nathans D: Cooperative transcriptional activity of Jun and Stat3 beta, a short form of Stat3. Proc Natl Acad Sci USA 1995, 92(20):9097-9101
28. Schuringa JJ, Timmer H, Luttickhuizen D, Vellenga E, Kruijer W: c-Jun and c-Fos cooperate with STAT3 in IL-6-induced transactivation of the IL-6 respone element (IRE). Cytokine 2001, 14(2):78-87
29. Schaefer TS, Sanders LK, Nathans D: Cooperative transcriptional activity of Jun and Stat3 beta, a short form of Stat3. Proc Natl Acad Sci USA 1995, 92(20):9097-9101
30. Vesely PW, Staber PB, Hoefler G, Kenner L: Translational regulation mechanisms of AP-1 proteins. Mutat Res 2009, 682:7-12
31. Oliviero S, Robinson GS, Struhl K, Spiegelman BM: Yeast GCN4 as a probe for oncogenesis by AP-1 transcription factors: transcriptional activation through AP-1 sites is not sufficient for cellular transformation. Genes Dev 1992, 6(9):1799-1809
32. MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E: An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 2006, 7:113
33. De Rijcke M, Seneca S, Punyammalee B, Glansdorff N, Crabeel M: Characterization of the DNA target site for the yeast ARGR regulatory complex, a se-quence able to mediate repression or induction by arginine. Mol Cell Biol 1992, 12:68-81
34. Dubois E, Messenguy F: Isolation and characterization of the yeast ARGRII gene involved in regu-lating both anabolism and catabolism of arginine. Mol Gen Genet 1985, 198(2):283-289
35. Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M: Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet 2008, 4(7):e1000133
36. van der Watt PJ, Leaner VD: The nuclear exporter, Crm1, is regulated by NFY and Sp1 in cancer cells and repressed by p53 in response to DNA damage. Biochim Biophys Acta 2011, 1809(7):316-326
37. Dalvai M, Mondesert O, Bourdon JC, Ducommun B, Dozier C: Cdc25B is negatively regulated by p53 through Sp1 and NF-Y transcription factors. Oncogene 2011, 30(19):2282-2288
38. Borestrom C, Zetterberg H, Liff K, Rymo L: Functional interaction of nuclear factor y and sp1 is required for activation of the epstein-barr virus C pro-moter. J Virol 2003, 77(2):821-829
39. Hayden MS, Ghosh S: NF-kB, the first quarter-century: remarkable progress and outstanding questions. Genes Dev 2012, 26:203-234
40. Ruefli-Brasse AA, French DM, Dixit VM: Regulation of NF-kappaBdependent lymphocyte activation and development by paracaspase. Science 2003, 302(5650):1581-1584
41. Kamiya M, Judson H, Okazaki Y, Kusakabe M, Mu-ramatsu M, Takada S, Takagi N, Arima T, Wake N, Kamimura K, Satomura K, Hermann R, Bonthron DT, Hayashizaki Y: The cell cycle control gene ZAC/PLAGL1 is imprinted-a strong candidate gene for transient neonatal diabetes. Hum Mol Genet 2000, 9(3):453-460
42. Meyer N, Penn LZ: Reflecting on 25 years with MYC. Nat Rev Cancer 2008, 8(12):976-990
43. Liu PY, Hsieh TY, Liu ST, Chang YL, Lin WS, Wang WM, Huang SM: Zac1, an Sp1-like protein, regulates human p21(WAF1/Cip1) gene expression in HeLa cells. Exp Cell Res 2011, 317(20):2925-2937
44. Jarmalaite S, Laurinaviciene A, Tverkuviene J, Kalin-auskaite N, Petroska D, Bohling T, Husgafvel-Pursiainen K: Tumor suppressor gene ZAC/PLAGL1: altered expression and loss of the nonimprinted allele in pheochromocytomas. Cancer Genet 2011, 204(7):398-404
45. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M: Mapping of transcription factor binding regions in mam-malian cells by ChIP: comparison of array-and sequencing-based technologies. Genome Res 2007, 17:898-909
46. Hudson ME, Snyder M: High-throughput methods of regulatory element discovery. BioTechniques 2006, 41, 673, 675, 677 passim
47. Pages H: BSgenome.Hsapiens.UCSC.hg19: Homo sapiens (Human) full genome (UCSC version hg19) 2011
48. Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A: JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res 2008, 36:D102-106
49. Newburger DE, Bulyk ML: UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 2009, 37:77-82
50. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, Durbin R, Eyras E, Gilbert J, Hammond M, Huminiecki L, Kasprzyk A, Lehvaslaiho H, Lijnzaad P, Melsopp C, Mon-gin E, Pettett R, Pocock M, Potter S, Rust A, Schmidt E, Searle S, Slater G, Smith J, Spooner W, Stabenau A, Stalker J, Stupka E, Ureta-Vidal A, Vastrik I, Clamp M: The Ensembl genome database project. Nucleic Acids Res 2002, 30:38-41
51. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K: Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 2008, 36: 5221-5231
52. Phillips JE, Corces VG: CTCF: master weaver of the genome. Cell 2009, 137:1194-1211
53. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Louki-nov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B: Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128:1231-1245
54. Grant CE, Bailey TL, Noble WS: FIMO: scanning for occurrences of a given motif. Bioinformatics 2011, 27:1017-1018
55. Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS: Quantifying similarity between motifs. Genome Biol 2007, 8:R24