The regulation and mechanism of transcription has been of great interest to researchers. In eukaryotic cells, DNA is packaged in the form of nucleosomal arrays. Each nucleosome core consists of 145 base pairs of DNA wound around an octamer of H2A, H2B, H3 and H4 histone proteins. These nucleosome cores are then packaged into higher order structures with additional factors to form chromatin (Luger, K. et al. Nature, 1997, 389, 251-60).
The incorporation of DNA into chromatin creates a repressive environment that has been implicated in transcriptional silencing. Two cellular processes serve to alter chromatin structure (Workman et al., Annu. Rev. Biochem., 1998, 67, 545-579). Chromatin remodeling factors such as SWI/SNF, RSC, NURF, and NRD (reviewed in Varga-Weisz, P. D. and Becker, P. B. Curr. Opin. Cell Biol., 1998, 10, 346-353; see also, Tong et al. Nature, 1998, 395, 917-921; Zhang et al. Cell, 1998, 95, 279-289; Xue et al., Mol. Cell, 1998, 2, 851-861) have been shown to increase the accessibility of the DNA, presumably by modifications of the nucleosomal structure. A second cellular mechanism involves alterations of the acetylation state of nucleosomal histones. Hypoacetylated chromatin is often associated with silent genes, while hyperacetylation is correlated with actively transcribed genes. However, this rule is not absolute. Acetylation of K12 on histone H4 is observed in silent heterochromatin regions in Drosophila and yeast (reviewed in Grunstein, M. Nature, 1997, 389, 349-352). Furthermore, there is increasing evidence for regulation of non-histone proteins by acetylation, and this may function in activation as well as repression of transcription (see, Imhof et al., Curr. Biol., 1997, 7, 689-692; Gu, W. and Roeder, R. G. Cell, 1997, 90, 595-606; Munshi et al. Mol. Cell, 1998, 2, 457-467). The acetylation state of histones and perhaps non-histone proteins is regulated by a dynamic interaction of histone acetyltransferase (HAT) and histone deacetylase (HDAC) enzymes.
Previously, three human HDACs (Taunton, J. et al. Science, 1996, 272, 408-411; Yang et al. J. Biol. Chem., 1997, 272, 28001-28007; Emiliani et al. Proc. Natl. Acad. Sci. USA, 1998, 95, 2795-2800; Dagond et al. Biochem. Biophys. Res. Commun., 1998, 242, 648-652) and five yeast HDACs (see, Rundlett et al. Proc. Natl. Acad. Sci USA, 1996, 93, 14503-14508; Carmen et al. J. Biol. Chem., 1996, 271, 15837-15844) had been identified and several of these were biochemically characterized. These HDACs, together with the prokaryotic enzymes acetylspermine deacetylase (ASD) and acetoin utilization protein (acuC) comprise a deacetylase superfamily. In yeast, members of this superfamily can be subdivided into two classes based on size and sequence considerations, as well as the observation that Rpd3p and Hda1p function in biochemically distinct complexes. The first class (I) consists of Rpd3p, Hos1p, and Hos2p, while the second class contains Hda1p. Similarly in mammals, HDAC1, HDAC2 and HDAC3 conform to class I criteria, while no human class II HDAC proteins have been identified previously.
Clearly, the identification of alternate classes of genes encoding histone deacetylase proteins would aid in the investigation of functions for these protein products, and thus would be of great benefit in the control of gene transcription and the cell cycle.