Histone deacetylase 1 and p300 can directly associate with chromatin and compete for binding in a mutually exclusive manner

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Li, Xuehui ^a   Yang, Hui ^a   Huang, Suming ^a   Qiu, Yi ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; E1A ASSOCIATED P300 PROTEIN; HISTONE DEACETYLASE 1; HISTONE H3; CHROMATIN; HDAC1 PROTEIN, HUMAN; HISTONE; HISTONE ACETYLTRANSFERASE PCAF; P300-CBP-ASSOCIATED FACTOR; PROTEIN BINDING;

ARTICLE; BINDING COMPETITION; BINDING SITE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME RECONSTITUTION; GENE EXPRESSION REGULATION; HISTONE ACETYLATION; IN VITRO STUDY; IN VIVO STUDY; NUCLEOSOME; PROTEIN BINDING; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION REGULATION; ACETYLATION; AMINO ACID SEQUENCE; CHEMISTRY; CYTOLOGY; EPITHELIUM CELL; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; TUMOR CELL LINE;

ACETYLATION; AMINO ACID SEQUENCE; BINDING SITES; BINDING, COMPETITIVE; CELL LINE, TUMOR; CHROMATIN; EPITHELIAL CELLS; GENE EXPRESSION REGULATION; HISTONE DEACETYLASE 1; HISTONES; HUMANS; MOLECULAR SEQUENCE DATA; P300-CBP TRANSCRIPTION FACTORS; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; TRANSCRIPTION, GENETIC;

EID: 84899574599     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094523     Document Type: Article

References (54)

1. Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64: 435-459. (Pubitemid 30412680)
2. Ng HH, Bird A (2000) Histone deacetylases: silencers for hire. Trends Biochem Sci 25: 121-126.
3. Yang XJ, Seto E (2008) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9: 206-218.
4. Cho Y, Griswold A, Campbell C, Min KT (2005) Individual histone deacetylases in Drosophila modulate transcription of distinct genes. Genomics 86: 606-617. (Pubitemid 41416792)
5. Foglietti C, Filocamo G, Cundari E, De Rinaldis E, Lahm A, et al. (2006) Dissecting the biological functions of Drosophila histone deacetylases by RNA interference and transcriptional profiling. J Biol Chem 281: 17968-17976. (Pubitemid 44035596)
6. Goodman RH, Smolik S (2000) CBP/p300 in cell growth, transformation, and development. Genes Dev 14: 1553-1577. (Pubitemid 30460905)
7. Eckner R (1996) p300 and CBP as transcriptional regulators and targets of oncogenic events. Biol Chem 377: 685-688.
8. Avantaggiati ML, Ogryzko V, Gardner K, Giordano A, Levine AS, et al. (1997) Recruitment of p300/CBP in p53-dependent signal pathways. Cell 89: 1175-1184. (Pubitemid 127678750)
9. Vo N, Goodman RH (2001) CREB-binding protein and p300 in transcriptional regulation. J Biol Chem 276: 13505-13508.
10. Simone C, Stiegler P, Forcales SV, Bagella L, De Luca A, et al. (2004) Deacetylase recruitment by the C/H3 domain of the acetyltransferase p300. Oncogene 23: 2177-2187. (Pubitemid 38482532)
11. Qiu Y, Zhao Y, Becker M, John S, Parekh BS, et al. (2006) HDAC1 acetylation is linked to progressive modulation of steroid receptor-induced gene transcription. Mol Cell 22: 669-679. (Pubitemid 43817601)
12. Richon VM, Sandhoff TW, Rifkind RA, Marks PA (2000) Histone deacetylase inhibitor selectively induces p21WAF1 expression and gene-associated histone acetylation. Proc Natl Acad Sci U S A 97: 10014-10019.
13. Wang Z, Zang C, Cui K, Schones DE, Barski A, et al. (2009) Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell 138: 1019-1031.
14. Perissi V, Jepsen K, Glass CK, Rosenfeld MG (2010) Deconstructing repression: evolving models of co-repressor action. Nat Rev Genet 11: 109-123.
15. Shahbazian MD, Grunstein M (2007) Functions of site-specific histone acetylation and deacetylation. Annu Rev Biochem 76: 75-100.
16. Kurdistani SK, Robyr D, Tavazoie S, Grunstein M (2002) Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nature genetics 31: 248-254.
17. Manning ET, Ikehara T, Ito T, Kadonaga JT, Kraus WL (2001) p300 forms a stable, template-committed complex with chromatin: role for the bromodomain. Molecular and cellular biology 21: 3876-3887. (Pubitemid 32476450)
18. Luo Y, Jian W, Stavreva D, Fu X, Hager G, et al. (2009) Trans-regulation of histone deacetylase activities through acetylation. J Biol Chem 284: 34901-34910.
19. Imbalzano AN, Kwon H, Green MR, Kingston RE (1994) Facilitated binding of TATA-binding protein to nucleosomal DNA. Nature 370: 481-485. (Pubitemid 24263556)
20. Workman JL, Taylor IC, Kingston RE, Roeder RG (1991) Control of class II gene transcription during in vitro nucleosome assembly. Methods in cell biology 35: 419-447.
21. Lowary PT, Widom J (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 276: 19-42. (Pubitemid 28085408)
22. Geisberg JV, Struhl K (2004) Quantitative sequential chromatin immunoprecipitation, a method for analyzing co-occupancy of proteins at genomic regions in vivo. Nucleic Acids Res 32: e151.
23. Geisberg JV, Struhl K (2005) Analysis of protein co-occupancy by quantitative sequential chromatin immunoprecipitation. Curr Protoc Mol Biol Chapter 21: Unit 21 28.
24. Kurdistani SK, Grunstein M (2003) Histone acetylation and deacetylation in yeast. Nature reviews Molecular cell biology 4: 276-284. (Pubitemid 36383954)
25. Zhang Y, Ng HH, Erdjument-Bromage H, Tempst P, Bird A, et al. (1999) Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev 13: 1924-1935. (Pubitemid 29407360)
26. Boyer LA, Latek RR, Peterson CL (2004) The SANT domain: a unique histone-tail-binding module? Nature reviews Molecular cell biology 5: 158-163. (Pubitemid 38160258)
27. Shi YJ, Matson C, Lan F, Iwase S, Baba T, et al. (2005) Regulation of LSD1 histone demethylase activity by its associated factors. Molecular cell 19: 857-864. (Pubitemid 41316679)
28. Grune T, Brzeski J, Eberharter A, Clapier CR, Corona DF, et al. (2003) Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol Cell 12: 449-460. (Pubitemid 37238931)
29. Liu Y, Peng L, Seto E, Huang S, Qiu Y (2012) Modulation of histone deacetylase 6 nuclear import and tubulin deacetylase activity through acetylation. J Biol Chem.
30. Yang XJ, Gregoire S (2005) Class II histone deacetylases: from sequence to function, regulation, and clinical implication. Mol Cell Biol 25: 2873-2884.
31. An W, Roeder RG (2003) Direct association of p300 with unmodified H3 and H4 N termini modulates p300-dependent acetylation and transcription of nucleosomal templates. J Biol Chem 278: 1504-1510. (Pubitemid 36801377)
32. Gui CY, Ngo L, Xu WS, Richon VM, Marks PA (2004) Histone deacetylase (HDAC) inhibitor activation of p21WAF1 involves changes in promoter-associated proteins, including HDAC1. Proc Natl Acad Sci U S A 101: 1241-1246. (Pubitemid 38182673)
33. Huang W, Zhao S, Ammanamanchi S, Brattain M, Venkatasubbarao K, et al. (2005) Trichostatin A induces transforming growth factor beta type II receptor promoter activity and acetylation of Sp1 by recruitment of PCAF/p300 to a Sp1.NF-Y complex. J Biol Chem 280: 10047-10054. (Pubitemid 40395856)
34. Rikitake Y, Moran E (1992) DNA-binding properties of the E1A-associated 300-kilodalton protein. Molecular and cellular biology 12: 2826-2836.
35. He S, Khan DH, Winter S, Seiser C, Davie JR (2013) Dynamic distribution of HDAC1 and HDAC2 during mitosis: Association with F-actin. Journal of cellular physiology 228: 1525-1535.
36. Robert F, Pokholok DK, Hannett NM, Rinaldi NJ, Chandy M, et al. (2004) Global position and recruitment of HATs and HDACs in the yeast genome. Molecular cell 16: 199-209. (Pubitemid 39388835)
37. Yang XJ, Seto E (2007) HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention. Oncogene 26: 5310-5318.
38. Drouin S, Laramee L, Jacques PE, Forest A, Bergeron M, et al. (2010) DSIF and RNA polymerase II CTD phosphorylation coordinate the recruitment of Rpd3S to actively transcribed genes. PLoS genetics 6: e1001173.
39. Govind CK, Qiu H, Ginsburg DS, Ruan C, Hofmeyer K, et al. (2010) Phosphorylated Pol II CTD recruits multiple HDACs, including Rpd3C(S), for methylation-dependent deacetylation of ORF nucleosomes. Molecular cell 39: 234-246.
40. Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, et al. (2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123: 593-605. (Pubitemid 41608463)
41. Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, et al. (2005) Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123: 581-592. (Pubitemid 41608462)
42. Li B, Gogol M, Carey M, Lee D, Seidel C, et al. (2007) Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science 316: 1050-1054. (Pubitemid 46799495)
43. Kim T, Buratowski S (2009) Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions. Cell 137: 259-272.
44. Tang Z, Chen WY, Shimada M, Nguyen UT, Kim J, et al. (2013) SET1 and p300 Act Synergistically, through Coupled Histone Modifications, in Transcriptional Activation by p53. Cell 154: 297-310.
45. Vogelauer M, Wu J, Suka N, Grunstein M (2000) Global histone acetylation and deacetylation in yeast. Nature 408: 495-498.
46. Kurdistani SK, Tavazoie S, Grunstein M (2004) Mapping global histone acetylation patterns to gene expression. Cell 117: 721-733. (Pubitemid 38748889)
47. Stavreva DA, Wiench M, John S, Conway-Campbell BL, McKenna MA, et al. (2009) Ultradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription. Nat Cell Biol 11: 1093-1102.
48. Degenhardt T, Vaisanen S, Rakhshandehroo M, Kersten S, Carlberg C (2009) Peroxisome proliferator-activated receptor alpha controls hepatic heme biosynthesis through ALAS1. Journal of molecular biology 388: 225-238.
49. Metivier R, Penot G, Hubner MR, Reid G, Brand H, et al. (2003) Estrogen receptor-alpha directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115: 751-763. (Pubitemid 38030303)
50. Qiu Y, Stavreva DA, Luo Y, Indrawan A, Chang M, et al. (2011) Dynamic Interaction of HDAC1 with a Glucocorticoid Receptor-regulated Gene Is Modulated by the Activity State of the Promoter. J Biol Chem 286: 7641-7647.
51. Hager GL, McNally JG, Misteli T (2009) Transcription dynamics. Mol Cell 35: 741-753.
52. Stavreva DA, Varticovski L, Hager GL (2012) Complex dynamics of transcription regulation. Biochimica et biophysica acta 1819: 657-666.
53. Yamagoe S, Kanno T, Kanno Y, Sasaki S, Siegel RM, et al. (2003) Interaction of histone acetylases and deacetylases in vivo. Mol Cell Biol 23: 1025-1033. (Pubitemid 36133518)
54. Girdwood D, Bumpass D, Vaughan OA, Thain A, Anderson LA, et al. (2003) P300 transcriptional repression is mediated by SUMO modification. Mol Cell 11: 1043-1054. (Pubitemid 36566325)