Isolation and Characterization of cDNAs Corresponding to an Additional Member of the Human Histone Deacetylase Gene Family

Several human cDNAs encoding a histone deacetylase protein, HDAC3, have been isolated. Analysis of the predicted amino acid sequence of HDAC3 revealed an open reading frame of 428 amino acids with a predicted molecular mass of 49 kDa. The HDAC3 protein is 50% identical in DNA sequence and 53% identical in protein sequence compared with the previously cloned human HDAC1. Comparison of the HDAC3 sequence with human HDAC2 also yielded similar results, with 51% identity in DNA sequence and 52% identity in protein sequence. The expressed HDAC3 protein is functionally active because it possesses histone deacetylase activity, represses transcription when tethered to a promoter, and binds transcription factor YY1. Similar to HDAC1 and HDAC2, HDAC3 is ubiquitously expressed in many different cell types. Several human cDNAs encoding a histone deacetylase protein, HDAC3, have been isolated. Analysis of the predicted amino acid sequence of HDAC3 revealed an open reading frame of 428 amino acids with a predicted molecular mass of 49 kDa. The HDAC3 protein is 50% identical in DNA sequence and 53% identical in protein sequence compared with the previously cloned human HDAC1. Comparison of the HDAC3 sequence with human HDAC2 also yielded similar results, with 51% identity in DNA sequence and 52% identity in protein sequence. The expressed HDAC3 protein is functionally active because it possesses histone deacetylase activity, represses transcription when tethered to a promoter, and binds transcription factor YY1. Similar to HDAC1 and HDAC2, HDAC3 is ubiquitously expressed in many different cell types. The organization of chromatin structure is a fundamental and significant component of transcriptional regulation in all eukaryotic cells. Transcriptionally active or repressed chromatin is determined, at least in part, by the modification of histones. For example, hyperacetylation of histones generally leads to an increase in transcription, whereas hypoacetylation of histones appears to have the opposite effect (reviewed in Refs. 1Brownell J.E. Allis C.D. Curr. Opin. Genet. Dev. 1996; 6: 176-184Crossref PubMed Scopus (463) Google Scholar, 2Wolffe A.P. Science. 1996; 272: 371-372Crossref PubMed Scopus (271) Google Scholar, 3Wade P.A. Wolffe A.P. Curr. Biol. 1997; 7: R82-R84Abstract Full Text Full Text PDF PubMed Google Scholar, 4Davie J.R. J. Cell. Biochem. 1996; 62: 149-157Crossref PubMed Scopus (43) Google Scholar). Nuclear histone acetyltransferases such as transcription factors GCN5, PCAF, p300/CBP, and TAFII230/250 have been identified from different organisms (5Brownell J.E. Zhou J. Ranalli T. Kobayashi R. Edmondson D.G. Roth S.Y. Allis C.D. Cell. 1996; 84: 843-851Abstract Full Text Full Text PDF PubMed Scopus (1277) Google Scholar, 6Mizzen C.A. Yang X.-J. Kokubo T. Brownell J.E. Bannister A.J. Owen-Hughes T. Workman J. Wang L. Berger S.L. Kouzarides T. Nakatani Y. Allis C.D. Cell. 1996; 87: 1261-1270Abstract Full Text Full Text PDF PubMed Scopus (617) Google Scholar, 7Bannister A.J. Kouzarides T. Nature. 1996; 384: 641-643Crossref PubMed Scopus (1523) Google Scholar, 8Ogryzko V.V. Schiltz R.L. Russanova V. Howard B.H. Nakatani Y. Cell. 1996; 87: 953-959Abstract Full Text Full Text PDF PubMed Scopus (2368) Google Scholar, 9Kuo M.H. Brownell J.E. Sobel R.E. Ranalli T.A. Cook R.G. Edmondson D.G. Roth S.Y. Allis C.D. Nature. 1996; 383: 269-272Crossref PubMed Scopus (503) Google Scholar).Several yeast and mammalian histone deacetylases have been identified, and their corresponding genes have been cloned (10Taunton J. Hassig C.A. Schreiber S.L. Science. 1996; 272: 408-411Crossref PubMed Scopus (1524) Google Scholar, 11Yang W.-M. Inouye C. Zeng Y. Bearss D. Seto E. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 12845-12850Crossref PubMed Scopus (482) Google Scholar, 12Rundlett S. Carmen A.A. Kobayashi R. Bavykin S. Turner B.M. Grunstein M. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 14503-14508Crossref PubMed Scopus (516) Google Scholar). In yeast, the HDA1 protein, which shares sequence similarity to RPD3, is a subunit of a large histone deacetylase complex HDA. RPD3 is also associated with another yeast histone deacetylase complex HDB. Using a trapoxin (an inhibitor of histone deacetylase) affinity matrix, Taunton et al. (10Taunton J. Hassig C.A. Schreiber S.L. Science. 1996; 272: 408-411Crossref PubMed Scopus (1524) Google Scholar) purified and cloned a human 55-kDa protein related to the yeast protein RPD3. Immunoprecipitation of this 55-kDa protein, HDAC1 (also called HD1), showed that it contains histone deacetylase activity. A second human histone deacetylase protein, HDAC2, with high homology to yeast RPD3 was identified based on a yeast two-hybrid trap experiment with the YY1 transcription factor as a bait (11Yang W.-M. Inouye C. Zeng Y. Bearss D. Seto E. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 12845-12850Crossref PubMed Scopus (482) Google Scholar). YY1 negatively regulates transcription by tethering HDAC2 to DNA as a corepressor. Both HDAC1 and HDAC2 exist in a complex with the corepressor mSIN3 and mediate Mad transcriptional repression (13Hassig C.A. Fleischer T.C. Billin A.N. Schreiber S.L. Ayer D.E. Cell. 1997; 89: 341-347Abstract Full Text Full Text PDF PubMed Scopus (656) Google Scholar, 14Laherty C.D. Yang W.-M. Sun J.-M. Davie J.R. Seto E. Eisenman R.N. Cell. 1997; 89: 349-356Abstract Full Text Full Text PDF PubMed Scopus (837) Google Scholar, 15Zhang Y. Iratni R. Erdjument-Bromage H. Tempst P. Reinberg D. Cell. 1997; 89: 357-364Abstract Full Text Full Text PDF PubMed Scopus (498) Google Scholar). In addition, HDAC1 and HDAC2 are essential components of two thyroid hormone receptor corepressors, N-CoR and SMRT (16Heinzel T. Lavinsky R.M. Mullen T.-M. Soderstrom M. Laherty C.D. Torchia J. Yang W.M. Brard G. Ngo S.D. Davie J.R. Seto E. Eisenman R.N. Rose D.W. Glass C.K. Rosenfeld M.G. Nature. 1997; 387: 43-48Crossref PubMed Scopus (1079) Google Scholar, 17Alland L. Muhle R. Hou H. Potes J. Chin L. Schreiber-Agus N. DePinho R.A. Nature. 1997; 387: 49-55Crossref PubMed Scopus (733) Google Scholar, 18Nagy L. Kao H.Y. Chakravarti D. Lin R.J. Hassig C.A. Ayer D.E. Schreiber S.L. Evans R.M. Cell. 1997; 89: 373-380Abstract Full Text Full Text PDF PubMed Scopus (1101) Google Scholar). HDAC1 is also an important factor that represses transactivation by progesterone receptor (19Jenster G. Spencer T.E. Burcin M.M. Tsai S.Y. Tsai M.-J. O'Malley B.W. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 7879-7884Crossref PubMed Scopus (231) Google Scholar).The yeast RPD3 protein was originally identified in genetic screens for transcriptional repressors (20Vidal M. Gaber R.F. Mol. Cell. Biol. 1991; 11: 6317-6327Crossref PubMed Scopus (261) Google Scholar). Besides human and mouse, highly homologous yeast RPD3 sequences have been identified inDrosophila (21Rubertis F.D. Kadosh D. Henchoz S. Pauli D. Reuter G. Struhl K. Spierer P. Nature. 1996; 384: 589-591Crossref PubMed Scopus (194) Google Scholar), Caenorhabditis elegans (X78454 and 1176665), and Xenopus laevis (gi:576995). Currently, it has not yet been established whether the C. elegans orX. laevis RPD3-related proteins have histone deacetylase activities or whether they play a role in transcriptional repression. Here, we describe the identification of a third human RPD3-related protein, HDAC3, that contains histone deacetylase activity. Like HDAC1 and HDAC2, HDAC3 represses transcription and binds transcription factor YY1, suggesting that it may participate in a large complex that mediates a wide variety of repression systems in human. The organization of chromatin structure is a fundamental and significant component of transcriptional regulation in all eukaryotic cells. Transcriptionally active or repressed chromatin is determined, at least in part, by the modification of histones. For example, hyperacetylation of histones generally leads to an increase in transcription, whereas hypoacetylation of histones appears to have the opposite effect (reviewed in Refs. 1Brownell J.E. Allis C.D. Curr. Opin. Genet. Dev. 1996; 6: 176-184Crossref PubMed Scopus (463) Google Scholar, 2Wolffe A.P. Science. 1996; 272: 371-372Crossref PubMed Scopus (271) Google Scholar, 3Wade P.A. Wolffe A.P. Curr. Biol. 1997; 7: R82-R84Abstract Full Text Full Text PDF PubMed Google Scholar, 4Davie J.R. J. Cell. Biochem. 1996; 62: 149-157Crossref PubMed Scopus (43) Google Scholar). Nuclear histone acetyltransferases such as transcription factors GCN5, PCAF, p300/CBP, and TAFII230/250 have been identified from different organisms (5Brownell J.E. Zhou J. Ranalli T. Kobayashi R. Edmondson D.G. Roth S.Y. Allis C.D. Cell. 1996; 84: 843-851Abstract Full Text Full Text PDF PubMed Scopus (1277) Google Scholar, 6Mizzen C.A. Yang X.-J. Kokubo T. Brownell J.E. Bannister A.J. Owen-Hughes T. Workman J. Wang L. Berger S.L. Kouzarides T. Nakatani Y. Allis C.D. Cell. 1996; 87: 1261-1270Abstract Full Text Full Text PDF PubMed Scopus (617) Google Scholar, 7Bannister A.J. Kouzarides T. Nature. 1996; 384: 641-643Crossref PubMed Scopus (1523) Google Scholar, 8Ogryzko V.V. Schiltz R.L. Russanova V. Howard B.H. Nakatani Y. Cell. 1996; 87: 953-959Abstract Full Text Full Text PDF PubMed Scopus (2368) Google Scholar, 9Kuo M.H. Brownell J.E. Sobel R.E. Ranalli T.A. Cook R.G. Edmondson D.G. Roth S.Y. Allis C.D. Nature. 1996; 383: 269-272Crossref PubMed Scopus (503) Google Scholar). Several yeast and mammalian histone deacetylases have been identified, and their corresponding genes have been cloned (10Taunton J. Hassig C.A. Schreiber S.L. Science. 1996; 272: 408-411Crossref PubMed Scopus (1524) Google Scholar, 11Yang W.-M. Inouye C. Zeng Y. Bearss D. Seto E. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 12845-12850Crossref PubMed Scopus (482) Google Scholar, 12Rundlett S. Carmen A.A. Kobayashi R. Bavykin S. Turner B.M. Grunstein M. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 14503-14508Crossref PubMed Scopus (516) Google Scholar). In yeast, the HDA1 protein, which shares sequence similarity to RPD3, is a subunit of a large histone deacetylase complex HDA. RPD3 is also associated with another yeast histone deacetylase complex HDB. Using a trapoxin (an inhibitor of histone deacetylase) affinity matrix, Taunton et al. (10Taunton J. Hassig C.A. Schreiber S.L. Science. 1996; 272: 408-411Crossref PubMed Scopus (1524) Google Scholar) purified and cloned a human 55-kDa protein related to the yeast protein RPD3. Immunoprecipitation of this 55-kDa protein, HDAC1 (also called HD1), showed that it contains histone deacetylase activity. A second human histone deacetylase protein, HDAC2, with high homology to yeast RPD3 was identified based on a yeast two-hybrid trap experiment with the YY1 transcription factor as a bait (11Yang W.-M. Inouye C. Zeng Y. Bearss D. Seto E. Proc. Natl. Acad. Sci. U. S. A. 1996; 93: 12845-12850Crossref PubMed Scopus (482) Google Scholar). YY1 negatively regulates transcription by tethering HDAC2 to DNA as a corepressor. Both HDAC1 and HDAC2 exist in a complex with the corepressor mSIN3 and mediate Mad transcriptional repression (13Hassig C.A. Fleischer T.C. Billin A.N. Schreiber S.L. Ayer D.E. Cell. 1997; 89: 341-347Abstract Full Text Full Text PDF PubMed Scopus (656) Google Scholar, 14Laherty C.D. Yang W.-M. Sun J.-M. Davie J.R. Seto E. Eisenman R.N. Cell. 1997; 89: 349-356Abstract Full Text Full Text PDF PubMed Scopus (837) Google Scholar, 15Zhang Y. Iratni R. Erdjument-Bromage H. Tempst P. Reinberg D. Cell. 1997; 89: 357-364Abstract Full Text Full Text PDF PubMed Scopus (498) Google Scholar). In addition, HDAC1 and HDAC2 are essential components of two thyroid hormone receptor corepressors, N-CoR and SMRT (16Heinzel T. Lavinsky R.M. Mullen T.-M. Soderstrom M. Laherty C.D. Torchia J. Yang W.M. Brard G. Ngo S.D. Davie J.R. Seto E. Eisenman R.N. Rose D.W. Glass C.K. Rosenfeld M.G. Nature. 1997; 387: 43-48Crossref PubMed Scopus (1079) Google Scholar, 17Alland L. Muhle R. Hou H. Potes J. Chin L. Schreiber-Agus N. DePinho R.A. Nature. 1997; 387: 49-55Crossref PubMed Scopus (733) Google Scholar, 18Nagy L. Kao H.Y. Chakravarti D. Lin R.J. Hassig C.A. Ayer D.E. Schreiber S.L. Evans R.M. Cell. 1997; 89: 373-380Abstract Full Text Full Text PDF PubMed Scopus (1101) Google Scholar). HDAC1 is also an important factor that represses transactivation by progesterone receptor (19Jenster G. Spencer T.E. Burcin M.M. Tsai S.Y. Tsai M.-J. O'Malley B.W. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 7879-7884Crossref PubMed Scopus (231) Google Scholar). The yeast RPD3 protein was originally identified in genetic screens for transcriptional repressors (20Vidal M. Gaber R.F. Mol. Cell. Biol. 1991; 11: 6317-6327Crossref PubMed Scopus (261) Google Scholar). Besides human and mouse, highly homologous yeast RPD3 sequences have been identified inDrosophila (21Rubertis F.D. Kadosh D. Henchoz S. Pauli D. Reuter G. Struhl K. Spierer P. Nature. 1996; 384: 589-591Crossref PubMed Scopus (194) Google Scholar), Caenorhabditis elegans (X78454 and 1176665), and Xenopus laevis (gi:576995). Currently, it has not yet been established whether the C. elegans orX. laevis RPD3-related proteins have histone deacetylase activities or whether they play a role in transcriptional repression. Here, we describe the identification of a third human RPD3-related protein, HDAC3, that contains histone deacetylase activity. Like HDAC1 and HDAC2, HDAC3 represses transcription and binds transcription factor YY1, suggesting that it may participate in a large complex that mediates a wide variety of repression systems in human. We thank Mon-Li Chu, Chris Hassig, Wen-Hwa Lee, Ivan Sadowski, Stuart Schreiber, Yang Shi, and Xueliang Zhu for generous gifts of plasmids and libraries and Nancy Olashaw and Tere Munoz-Antonia for discussion and critical reading of the manuscript.