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Gene Review

HDA1  -  Hda1p

Saccharomyces cerevisiae S288c

Synonyms: Histone deacetylase HDA1, N2819, YNL021W
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High impact information on HDA1

  • The epigenetic state of FLO11 is heritable for many generations and regulated by the histone deacetylase (HDAC) Hda1p [1].
  • Rpd3 and Hda1 deacetylate mainly distinct promoters and gene classes where they are recruited largely by novel mechanisms [2].
  • Hda1 also deacetylates subtelomeric domains containing normally repressed genes that are used instead for gluconeogenesis, growth on carbon sources other than glucose, and adverse growth conditions [2].
  • It is also shown that TUP1 interacts with HDA1 in vitro [3].
  • We report that in vivo increased acetylation of the repressed Saccharomyces cerevisiae ADH2 promoter chromatin, as obtained by disrupting the genes for the two deacetylases HDA1 and RPD3, destabilizes the structure of the TATA box-containing nucleosome [4].

Biological context of HDA1

  • Histone deacetylase HDA1, the prototype for the class II mammalian deacetylases, is likely the catalytic subunit of the HDA1-containing complex that is involved in TUP1-specific repression and global deacetylation in yeast [5].
  • We find that both hda1 and rpd3 deletions increase acetylation levels in vivo at all sites examined in both core histones H3 and H4, with rpd3 deletions having a greater impact on histone H4 lysine positions 5 and 12 [6].
  • Suppressor analysis of a histone defect identifies a new function for the hda1 complex in chromosome segregation [7].
  • Our results show that Hda3 has functions distinct from Hda2 and Hda1 and that it is required for normal chromosome segregation and cell cycle progression [7].
  • In support of this conclusion, gcn5Deltaelp3Delta phenotypes are suppressed by concomitant mutation of the HDA1 and HOS2 histone deacetylases [8].

Associations of HDA1 with chemical compounds

  • Searches of several sequence databases reveal that human HD1, yeast HDA1, yeast RPD3 and other eukaryotic histone deacetylases share nine motifs with archaeal and eubacterial enzymes, including acetoin utilization protein (acuC) and acetylpolyamine amidohydrolase [9].
  • Srb10 (a cyclin-dependent kinase associated with the Mediator complex) and Hda1 (a class I histone deacetylase) have each been implicated in Tup1-mediated repression [10].

Physical interactions of HDA1


Other interactions of HDA1

  • The HDA1 protein (a subunit of the HDA activity) shares sequence similarity to RPD3, a factor required for optimal transcription of certain yeast genes [6].
  • These findings suggest that the Hda1 deacetylase complex affects histone function at the centromere and that Hda3 has a distinctive participation in chromosome segregation [7].
  • These data indicate that TUP1 mediates localized histone deacetylation through HDA1 [3].
  • The results suggest that Rpd3p affects both processes that play an obligate and those that play a synergistic role in life extension by caloric restriction, while Hda1p and Sir2p affect processes that are not the obligate longevity effectors of caloric restriction but instead synergize with them, although in opposite directions [11].
  • Deletion of HDA1, another histone deacetylase gene, did not result in life-span extension, unless it was combined with deletion of SIR3 [12].

Analytical, diagnostic and therapeutic context of HDA1


  1. Genetic and epigenetic regulation of the FLO gene family generates cell-surface variation in yeast. Halme, A., Bumgarner, S., Styles, C., Fink, G.R. Cell (2004) [Pubmed]
  2. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Robyr, D., Suka, Y., Xenarios, I., Kurdistani, S.K., Wang, A., Suka, N., Grunstein, M. Cell (2002) [Pubmed]
  3. TUP1 utilizes histone H3/H2B-specific HDA1 deacetylase to repress gene activity in yeast. Wu, J., Suka, N., Carlson, M., Grunstein, M. Mol. Cell (2001) [Pubmed]
  4. Hyperacetylation of chromatin at the ADH2 promoter allows Adr1 to bind in repressed conditions. Verdone, L., Wu, J., van Riper, K., Kacherovsky, N., Vogelauer, M., Young, E.T., Grunstein, M., Di Mauro, E., Caserta, M. EMBO J. (2002) [Pubmed]
  5. HDA2 and HDA3 are related proteins that interact with and are essential for the activity of the yeast histone deacetylase HDA1. Wu, J., Carmen, A.A., Kobayashi, R., Suka, N., Grunstein, M. Proc. Natl. Acad. Sci. U.S.A. (2001) [Pubmed]
  6. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Rundlett, S.E., Carmen, A.A., Kobayashi, R., Bavykin, S., Turner, B.M., Grunstein, M. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  7. Suppressor analysis of a histone defect identifies a new function for the hda1 complex in chromosome segregation. Kanta, H., Laprade, L., Almutairi, A., Pinto, I. Genetics (2006) [Pubmed]
  8. Overlapping roles for the histone acetyltransferase activities of SAGA and elongator in vivo. Wittschieben, B.O., Fellows, J., Du, W., Stillman, D.J., Svejstrup, J.Q. EMBO J. (2000) [Pubmed]
  9. Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily. Leipe, D.D., Landsman, D. Nucleic Acids Res. (1997) [Pubmed]
  10. Promoter-dependent roles for the Srb10 cyclin-dependent kinase and the Hda1 deacetylase in Tup1-mediated repression in Saccharomyces cerevisiae. Green, S.R., Johnson, A.D. Mol. Biol. Cell (2004) [Pubmed]
  11. Distinct roles of processes modulated by histone deacetylases Rpd3p, Hda1p, and Sir2p in life extension by caloric restriction in yeast. Jiang, J.C., Wawryn, J., Shantha Kumara, H.M., Jazwinski, S.M. Exp. Gerontol. (2002) [Pubmed]
  12. Modulation of life-span by histone deacetylase genes in Saccharomyces cerevisiae. Kim, S., Benguria, A., Lai, C.Y., Jazwinski, S.M. Mol. Biol. Cell (1999) [Pubmed]
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