Genomic occupancy of the transcriptional co-activators p300 and CBP

Transcription

Volumn 4, Issue 1, 2013, Pages 18-23

  Holmqvist, Per Henrik ^a   Mannervik, Mattias ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

CBP; ChIP seq; Enhancer; p300; Polycomb; Transcription

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN BINDING PROTEIN; DECAPENTAPLEGIC PROTEIN; DNA; E1A ASSOCIATED P300 PROTEIN; HISTONE H3; POSITIVE TRANSCRIPTION ELONGATION FACTOR B; SMAD PROTEIN;

ARTICLE; BINDING SITE; CHROMATIN; EMBRYO DEVELOPMENT; ENHANCER REGION; ENZYME ACTIVITY; GENE ACTIVATION; GENE REPRESSION; HISTONE ACETYLATION; NONHUMAN; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

METAZOA;

EID: 84872198371     PISSN: 21541264     EISSN: 21541272     Source Type: Journal    
DOI: 10.4161/trns.22601     Document Type: Article

References (55)

1. Chrivia JC, Kwok RP, Lamb N, Hagiwara M, Montminy MR, Goodman RH. Phosphorylated CREB binds specifically to the nuclear protein CBP. Nature 1993; 365:855-9; PMID:8413673; http://dx.doi.org/10.1038/365855a0.
2. Eckner R, Ewen ME, Newsome D, Gerdes M, DeCaprio JA, Lawrence JB, et al. Molecular cloning and functional analysis of the adenovirus E1A-associated 300-kD protein (p300) reveals a protein with properties of a transcriptional adaptor. Genes Dev 1994; 8:869-84; PMID:7523245; http://dx.doi.org/10.1101/gad.8.8.869.
3. Whyte P, Williamson NM, Harlow E. Cellular targets for transformation by the adenovirus E1A proteins. Cell 1989; 56:67-75; PMID:2521301; http://dx.doi.org/10.1016/0092-8674(89)90984-7.
4. Bedford DC, Kasper LH, Fukuyama T, Brindle PK. Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases. Epigenetics 2010; 5:9-15; PMID:20110770; http://dx.doi.org/10.4161/epi.5.1.10449.
5. Wang L, Tang Y, Cole PA, Marmorstein R. Structure and chemistry of the p300/CBP and Rtt109 histone acetyltransferases: implications for histone acetyltransferase evolution and function. Curr Opin Struct Biol 2008; 18:741-7; PMID:18845255; http://dx.doi.org/10.1016/j.sbi.2008.09.004.
6. Jin Q, Yu LR, Wang L, Zhang Z, Kasper LH, Lee JE, et al. Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation. EMBO J 2011; 30:249-62; PMID:21131905; http://dx.doi.org/10.1038/emboj.2010.318.
7. Tie F, Banerjee R, Stratton CA, Prasad-Sinha J, Stepanik V, Zlobin A, et al. CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development 2009; 136:3131-41; PMID:19700617; http://dx.doi.org/10.1242/dev.037127.
8. Das C, Lucia MS, Hansen KC, Tyler JK. CBP/p300-mediated acetylation of histone H3 on lysine 56. Nature 2009; 459:113-7; PMID:19270680; http://dx.doi.org/10.1038/nature07861.
9. Zeng L, Zhang Q, Gerona-Navarro G, Moshkina N, Zhou MM. Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. Structure 2008; 16:643-52; PMID:18400184; http://dx.doi.org/10.1016/j.str.2008.01.010.
10. Goodman RH, Smolik S. CBP/p300 in cell growth, transformation, and development. Genes Dev 2000; 14:1553-77; PMID:10887150.
11. Horwitz GA, Zhang K, McBrian MA, Grunstein M, Kurdistani SK, Berk AJ. Adenovirus small e1a alters global patterns of histone modification. Science 2008; 321:1084-5; PMID:18719283; http://dx.doi.org/10.1126/science.1155544.
12. Ferrari R, Su T, Li B, Bonora G, Oberai A, Chan Y, et al. Reorganization of the host epigenome by a viral oncogene. Genome Res 2012; 22:1212-21; PMID:22499665; http://dx.doi.org/10.1101/gr.132308.111.
13. Roelfsema JH, Peters DJ. Rubinstein-Taybi syndrome: clinical and molecular overview. Expert Rev Mol Med 2007; 9:1-16; PMID:17942008; http://dx.doi.org/10.1017/S1462399407000415.
14. Iyer NG, Ozdag H, Caldas C. p300/CBP and cancer. Oncogene 2004; 23:4225-31; PMID:15156177; http://dx.doi.org/10.1038/sj.onc.1207118.
15. Mullighan CG, Zhang J, Kasper LH, Lerach S, Payne-Turner D, Phillips LA, et al. CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 2011; 471:235-9; PMID:21390130; http://dx.doi.org/10.1038/nature09727.
16. Pasqualucci L, Dominguez-Sola D, Chiarenza A, Fabbri G, Grunn A, Trifonov V, et al. Inactivating mutations of acetyltransferase genes in B-cell lymphoma. Nature 2011; 471:189-95; PMID:21390126; http://dx.doi.org/10.1038/nature09730.
17. Wang Z, Zang C, Cui K, Schones DE, Barski A, Peng W, et al. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 2009; 138:1019-31; PMID:19698979; http://dx.doi.org/10.1016/j.cell.2009.06.049.
18. Ramos YF, Hestand MS, Verlaan M, Krabbendam E, Ariyurek Y, van Galen M, et al. Genome-wide assessment of differential roles for p300 and CBP in transcription regulation. Nucleic Acids Res 2010; 38:5396-408; PMID:20435671; http://dx.doi.org/10.1093/nar/gkq184.
19. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 2007; 39:311-8; PMID:17277777; http://dx.doi.org/10.1038/ng1966.
20. Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, et al. A cis-regulatory map of the Drosophila genome. Nature 2011; 471:527-31; PMID:21430782; http://dx.doi.org/10.1038/nature09990.
21. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009; 457:854-8; PMID:19212405; http://dx.doi.org/10.1038/nature07730.
22. Ong CT, Corces VG. Enhancer function: new insights into the regulation of tissue-specific gene expression. Nat Rev Genet 2011; 12:283-93; PMID:21358745; http://dx.doi.org/10.1038/nrg2957.
23. Holmqvist PH, Boija A, Philip P, Crona F, Stenberg P, Mannervik M. Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos. PLoS Genet 2012; 8:e1002769; PMID:22737084; http://dx.doi.org/10.1371/journal.pgen.1002769.
24. Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell 2011; 44:410-23; PMID:22055187; http://dx.doi.org/10.1016/j.molcel.2011.08.037.
25. Yao TP, Oh SP, Fuchs M, Zhou ND, Ch'ng LE, Newsome D, et al. Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300. Cell 1998; 93:361-72; PMID:9590171; http://dx.doi.org/10.1016/S0092-8674(00)81165-4.
26. Hong JW, Hendrix DA, Papatsenko D, Levine MS. How the Dorsal gradient works: insights from postgenome technologies. Proc Natl Acad Sci U S A 2008; 105:20072-6; PMID:19104040; http://dx.doi.org/10.1073/pnas.0806476105.
27. Affolter M, Marty T, Vigano MA, Jaźwiźska A. Nuclear interpretation of Dpp signaling in Drosophila. EMBO J 2001; 20:3298-305; PMID:11432817; http://dx.doi.org/10.1093/emboj/20.13.3298.
28. Akimaru H, Hou DX, Ishii S. Drosophila CBP is required for dorsal-dependent twist gene expression. Nat Genet 1997; 17:211-4; PMID:9326945; http://dx.doi.org/10.1038/ng1097-211.
29. Fu D, Ma J. Interplay between positive and negative activities that influence the role of Bicoid in transcription. Nucleic Acids Res 2005; 33:3985-93; PMID:16030350; http://dx.doi.org/10.1093/nar/gki691.
30. Fu D, Wen Y, Ma J. The co-activator CREB-binding protein participates in enhancer-dependent activities of bicoid. J Biol Chem 2004; 279:48725-33; PMID:15358774; http://dx.doi.org/10.1074/jbc.M407066200.
31. Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, et al.; modENCODE Consortium. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010; 330:1787-97; PMID:21177974; http://dx.doi.org/10.1126/science.1198374.
32. Kvon EZ, Stampfel G, Yáñez-Cuna JO, Dickson BJ, Stark A. HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev 2012; 26:908-13; PMID:22499593; http://dx.doi.org/10.1101/gad.188052.112.
33. Byun JS, Wong MM, Cui W, Idelman G, Li Q, De Siervi A, et al. Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes. Proc Natl Acad Sci U S A 2009; 106:19286-91; PMID:19880750; http://dx.doi.org/10.1073/pnas.0905469106.
34. Ceschin DG, Walia M, Wenk SS, Duboé C, Gaudon C, Xiao Y, et al. Methylation specifies distinct estrogen-induced binding site repertoires of CBP to chromatin. Genes Dev 2011; 25:1132-46; PMID:21632823; http://dx.doi.org/10.1101/gad.619211.
35. Rikitake Y, Moran E. DNA-binding properties of the E1A-associated 300-kilodalton protein. Mol Cell Biol 1992; 12:2826-36; PMID:1534143.
36. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A 2010; 107:21931-6; PMID:21106759; http://dx.doi.org/10.1073/pnas.1016071107.
37. Rada-Iglesias A, Bajpai R, Swigut T, Brugmann SA, Flynn RA, Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2011; 470:279-83; PMID:21160473; http://dx.doi.org/10.1038/nature09692.
38. Zentner GE, Tesar PJ, Scacheri PC. Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 2011; 21:1273-83; PMID:21632746; http://dx.doi.org/10.1101/gr.122382.111.
39. Bell O, Schwaiger M, Oakeley EJ, Lienert F, Beisel C, Stadler MB, et al. Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing. Nat Struct Mol Biol 2010; 17:894-900; PMID:20562853; http://dx.doi.org/10.1038/nsmb.1825.
40. Simon JA, Kingston RE. Mechanisms of polycomb gene silencing: knowns and unknowns. Nat Rev Mol Cell Biol 2009; 10:697-708; PMID:19738629.
41. Kim WJ, Rivera MN, Coffman EJ, Haber DA. The WTX tumor suppressor enhances p53 acetylation by CBP/p300. Mol Cell 2012; 45:587-97; PMID:22285752; http://dx.doi.org/10.1016/j.molcel.2011.12.025.
42. Chen J, Li Q. Life and death of transcriptional co-activator p300. Epigenetics 2011; 6:957-61; PMID:21730760; http://dx.doi.org/10.4161/epi.6.8.16065.
43. Thompson PR, Wang D, Wang L, Fulco M, Pediconi N, Zhang D, et al. Regulation of the p300 HAT domain via a novel activation loop. Nat Struct Mol Biol 2004; 11:308-15; PMID:15004546; http://dx.doi.org/10.1038/nsmb740.
44. Grossman SR, Deato ME, Brignone C, Chan HM, Kung AL, Tagami H, et al. Polyubiquitination of p53 by a ubiquitin ligase activity of p300. Science 2003; 300:342-4; PMID:12690203; http://dx.doi.org/10.1126/science.1080386.
45. Shi D, Pop MS, Kulikov R, Love IM, Kung AL, Grossman SR. CBP and p300 are cytoplasmic E4 polyubiquitin ligases for p53. Proc Natl Acad Sci U S A 2009; 106:16275-80; PMID:19805293; http://dx.doi.org/10.1073/pnas.0904305106.
46. Pasini D, Malatesta M, Jung HR, Walfridsson J, Willer A, Olsson L, et al. Characterization of an antagonistic switch between histone H3 lysine 27 methylation and acetylation in the transcriptional regulation of Polycomb group target genes. Nucleic Acids Res 2010; 38:4958-69; PMID:20385584; http://dx.doi.org/10.1093/nar/gkq244.
47. Tie F, Banerjee R, Conrad PA, Scacheri PC, Harte PJ. Histone demethylase UTX and chromatin remodeler BRM bind directly to CBP and modulate acetylation of histone H3 lysine 27. Mol Cell Biol 2012; 32:2323-34; PMID:22493065; http://dx.doi.org/10.1128/MCB.06392-11.
48. Kasper LH, Lerach S, Wang J, Wu S, Jeevan T, Brindle PK. CBP/p300 double null cells reveal effect of coactivator level and diversity on CREB transactivation. EMBO J 2010; 29:3660-72; PMID:20859256; http://dx.doi.org/10.1038/emboj.2010.235.
49. Cho H, Orphanides G, Sun X, Yang XJ, Ogryzko V, Lees E, et al. A human RNA polymerase II complex containing factors that modify chromatin structure. Mol Cell Biol 1998; 18:5355-63; PMID:9710619.
50. Kwok RP, Lundblad JR, Chrivia JC, Richards JP, Bächinger HP, Brennan RG, et al. Nuclear protein CBP is a coactivator for the transcription factor CREB. Nature 1994; 370:223-6; PMID:7913207; http://dx.doi.org/10.1038/370223a0.
51. Crump NT, Hazzalin CA, Bowers EM, Alani RM, Cole PA, Mahadevan LC. Dynamic acetylation of all lysine-4 trimethylated histone H3 is evolutionarily conserved and mediated by p300/CBP. Proc Natl Acad Sci U S A 2011; 108:7814-9; PMID:21518915; http://dx.doi.org/10.1073/pnas.1100099108.
52. Cho S, Schroeder S, Kaehlcke K, Kwon HS, Pedal A, Herker E, et al. Acetylation of cyclin T1 regulates the equilibrium between active and inactive P-TEFb in cells. EMBO J 2009; 28:1407-17; PMID:19387490; http://dx.doi.org/10.1038/emboj.2009.99.
53. Fu J, Yoon HG, Qin J, Wong J. Regulation of P-TEFb elongation complex activity by CDK9 acetylation. Mol Cell Biol 2007; 27:4641-51; PMID:17452463; http://dx.doi.org/10.1128/MCB.00857-06.
54. Lilja T, Aihara H, Stabell M, Nibu Y, Mannervik M. The acetyltransferase activity of Drosophila CBP is dispensable for regulation of the Dpp pathway in the early embryo. Dev Biol 2007; 305:650-8; PMID:17336283; http://dx.doi.org/10.1016/j.ydbio.2007.01.036.
55. Lilja T, Qi D, Stabell M, Mannervik M. The CBP coactivator functions both upstream and downstream of Dpp/Screw signaling in the early Drosophila embryo. Dev Biol 2003; 262:294-302; PMID:14550792; http://dx.doi.org/10.1016/S0012-1606(03)00392-0.