HCFC1 is a common component of active human CpG-island promoters and coincides with ZNF143, THAP11, YY1, and GABP transcription factor occupancy

Genome Research

Volumn 23, Issue 6, 2013, Pages 907-916

  Michaud, Joëlle ^a,c   Praz, Viviane ^a   Faresse, Nicole James ^a   JnBaptiste, Courtney K ^a,d   Tyagi, Shweta ^a,e   Schütz, Frédéric ^b   Herr, Winship ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c EPFL   (Switzerland)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

GA BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR HCFC1; TRANSCRIPTION FACTOR THAP11; TRANSCRIPTION FACTOR YY1; TRANSCRIPTION FACTOR ZNF143; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; CPG ISLAND; DNA SEQUENCE; FEMALE; HELA CELL; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; TRANSCRIPTION REGULATION;

BASE SEQUENCE; BINDING SITES; CPG ISLANDS; GA-BINDING PROTEIN TRANSCRIPTION FACTOR; GENE EXPRESSION REGULATION; HELA CELLS; HOST CELL FACTOR C1; HUMANS; NUCLEOTIDE MOTIFS; POSITION-SPECIFIC SCORING MATRICES; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REPRESSOR PROTEINS; RNA, MESSENGER; SIGNAL TRANSDUCTION; TRANS-ACTIVATORS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTIONAL ACTIVATION; YY1 TRANSCRIPTION FACTOR;

SIMPLEXVIRUS;

EID: 84878689941     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.150078.112     Document Type: Article

References (45)

1. Allen MD, Grummitt CG, Hilcenko C, Min SY, Tonkin LM, Johnson CM, Freund SM, Bycroft M, Warren AJ. 2006. Solution structure of the nonmethyl-CpG-binding CXXC domain of the leukaemia-associated MLL histone methyltransferase. EMBO J 25: 4503-4512. (Pubitemid 44498124)
2. Anno YN, Myslinski E, Ngondo-Mbongo RP, Krol A, Poch O, Lecompte O, Carbon P. 2011. Genome-wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription. Nucleic Acids Res 39: 3116-3127.
3. Antequera F, Bird A. 1999. CpG islands as genomic footprints of promoters that are associated with replication origins. Curr Biol 9: R661-R667. (Pubitemid 29442475)
4. Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
5. Bailey TL, Gribskov M. 1998. Combining evidence using P-values: Application to sequence homology searches. Bioinformatics 14: 48-54. (Pubitemid 28395676)
6. Bannister AJ, Schneider R, Myers FA, Thorne AW, Crane-Robinson C, Kouzarides T. 2005. Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J Biol Chem 280: 17732-17736. (Pubitemid 41389011)
7. Capotosti F, Guernier S, Lammers F, Waridel P, Cai Y, Jin J, Conaway JW, Conaway RC, HerrW. 2011. O-GlcNAc transferase catalyzes site-specific proteolysis of HCF-1. Cell 144: 376-388.
8. Chen X, Fang F, Liou YC, Ng HH. 2008. Zfp143 regulates Nanog through modulation of Oct4 binding. Stem Cells 26: 2759-2767.
9. Dejosez M, Krumenacker JS, Zitur LJ, Passeri M, Chu LF, Songyang Z, Thomson JA, Zwaka TP. 2008. Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. Cell 133: 1162-1174. (Pubitemid 351852919)
10. Dejosez M, Levine SS, Frampton GM, Whyte WA, Stratton SA, Barton MC, Gunaratne PH, Young RA, Zwaka TP. 2010. Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev 24: 1479-1484.
11. Freiman RN, Herr W. 1997. Viral mimicry: Common mode of association with HCF by VP16 and the cellular protein LZIP. Genes Dev 11: 3122-3127. (Pubitemid 27528053)
12. Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T, et al. 2002. The Ensembl genome database project. Nucleic Acids Res 30: 38-41. (Pubitemid 34679498)
13. Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP. 2010. Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet 6: e1001134.
14. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
15. Iseli C, Ambrosini G, Bucher P, Jongeneel CV. 2007. Indexing strategies for rapid searches of short words in genome sequences. PLoS ONE 2: e579.
16. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. 2008. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-seq data. Nucleic Acids Res 36: 5221-5231.
17. Julien E, Herr W. 2003. Proteolytic processing is necessary to separate and ensure proper cell growth and cytokinesis functions of HCF-1. EMBO J 22: 2360-2369. (Pubitemid 36604975)
18. Khurana B, Kristie TM. 2004. A protein sequestering system reveals control of cellular programs by the transcriptional coactivator HCF-1. J Biol Chem 279: 33673-33683. (Pubitemid 39063017)
19. Knez J, Piluso D, Bilan P, Capone JP. 2006. Host cell factor-1 and E2F4 interact via multiple determinants in each protein. Mol Cell Biochem 288: 79-90. (Pubitemid 44314443)
20. Kristie TM, Liang Y, Vogel JL. 2010. Control of a-herpesvirus IE gene expression by HCF-1 coupled chromatin modification activities. Biochim Biophys Acta 1799: 257-265.
21. Lee JH, Skalnik DG. 2005. CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex. J Biol Chem 280: 41725-41731. (Pubitemid 41832235)
22. Lemon B, Tjian R. 2000. Orchestrated response: A symphony of transcription factors for gene control. Genes Dev 14: 2551-2569.
23. Lu R, Yang P, Padmakumar S, Misra V. 1998. The herpesvirus transactivator VP16 mimics a human basic domain leucine zipper protein, luman, in its interaction with HCF. J Virol 72: 6291-6297. (Pubitemid 28323938)
24. Machida YJ, Machida Y, Vashisht AA, Wohlschlegel JA, Dutta A. 2009. The deubiquitinating enzyme BAP1 regulates cell growth via interaction with HCF-1. J Biol Chem 284: 34179-34188.
25. Mahony S, Benos PV. 2007. STAMP: A web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 35: W253-W258.
26. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, et al. 2006. TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34: D108-D110.
27. Park J, Lammers F, Herr W, Song JJ. 2012. HCF-1 self-association via an interdigitated Fn3 structure facilitates transcriptional regulatory complex formation. Proc Natl Acad Sci 109: 17430-17435.
28. Ramos YF, Hestand MS, Verlaan M, Krabbendam E, Ariyurek Y, van Galen M, van Dam H, van Ommen GJ, den Dunnen JT, Zantema A, et al. 2010. Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. Nucleic Acids Res 38: 5396-5408.
29. Ruppert SM, McCulloch V, Meyer M, Bautista C, Falkowski M, Stunnenberg HG, Hernandez N. 1996. Monoclonal antibodies directed against the amino-terminal domain of human TBP cross-react with TBP from other species. Hybridoma 15: 55-68. (Pubitemid 26079725)
30. Schaub M, Krol A, Carbon P. 1999. Flexible zinc finger requirement for binding of the transcriptional activator Staf to U6 small nuclear RNA and tRNASec promoters. J Biol Chem 274: 24241-24249.
31. Schenk PM, Baumann S, Mattes R, Steinbiss HH. 1995. Improved high-level expression system for eukaryotic genes in Escherichia coli using T7 RNA polymerase and rare ArgtRNAs. BioTechniques 19: 196-200.
32. Smyth GK. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
33. Tighe A, Johnson VL, Taylor SS. 2004. Truncating APC mutations have dominant effects on proliferation, spindle checkpoint control, survival and chromosome stability. J Cell Sci 117: 6339-6353. (Pubitemid 40214561)
34. Tyagi S, Chabes AL, Wysocka J, Herr W. 2007. E2F activation of S phase promoters via association with HCF-1 and the MLL family of histone H3K4 methyltransferases. Mol Cell 27: 107-119. (Pubitemid 46991384)
35. 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.
36. Vogel JL, Kristie TM. 2000. The novel coactivator C1 (HCF) coordinates multiprotein enhancer formation and mediates transcription activation by GABP. EMBO J 19: 683-690. (Pubitemid 30093741)
37. Wilson AC, LaMarco K, Peterson MG, Herr W. 1993. The VP16 accessory protein HCF is a family of polypeptides processed from a large precursor protein. Cell 74: 115-125. (Pubitemid 23219883)
38. Wysocka J, HerrW. 2003. The herpes simplex virus VP16-induced complex: The makings of a regulatory switch. Trends Biochem Sci 28: 294-304. (Pubitemid 36776292)
39. Wysocka J, Reilly PT, Herr W. 2001. Loss of HCF-1-chromatin association precedes temperature-induced growth arrest of tsBN67 cells. Mol Cell Biol 21: 3820-3829. (Pubitemid 32466993)
40. Wysocka J, Myers MP, Laherty CD, Eisenman RN, Herr W. 2003. Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes Dev 17: 896-911. (Pubitemid 36397377)
41. Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, Roeder RG, Brivanlou AH, Allis CD. 2005. WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121: 859-872. (Pubitemid 40806418)
42. Yang ZF, Mott S, Rosmarin AG. 2007. The Ets transcription factor GABP is required for cell-cycle progression. Nat Cell Biol 9: 339-346. (Pubitemid 46344614)
43. Yu H,Mashtalir N, Daou S, Hammond-Martel I, Ross J, Sui G, Hart GW, Rauscher FJ III, Drobetsky E, Milot E, et al. 2010. The ubiquitin carboxyl hydrolase BAP1 forms a ternary complex with YY1 and HCF-1 and is a critical regulator of gene expression.Mol Cell Biol 30: 5071-5085.
44. Yuan CC, Zhao X, Florens L, Swanson SK, Washburn MP, Hernandez N. 2007. CHD8 associates with human Staf and contributes to efficient U6 RNA polymerase III transcription. Mol Cell Biol 27: 8729-8738.
45. Zargar Z, Tyagi S. 2012. Role of Host Cell Factor-1 in cell cycle regulation. Transcription 3: 187-192.