Abstract
In yeast, Hda1 histone deacetylase complex (Hda1C) preferentially deacetylates histones H3 and H2B, and functionally interacts with Tup1 to repress transcription. However, previous studies identified global increases in histone H4 acetylation in cells lacking Hda1, a component of Hda1C. Here, we find that Hda1C binds to hyperactive genes, likely via the interaction between the Arb2 domain of Hda1 and RNA polymerase II. Additionally, we report that Hda1C specifically deacetylates H4, but not H3, at hyperactive genes to partially inhibit elongation. This role is contrast to that of the Set2–Rpd3S pathway deacetylating histones at infrequently transcribed genes. We also find that Hda1C deacetylates H3 at inactive genes to delay the kinetics of gene induction. Therefore, in addition to fine-tuning of transcriptional response via H3-specific deacetylation, Hda1C may modulate elongation by specifically deacetylating H4 at highly transcribed regions.
Highlights
In yeast, Hda[1] histone deacetylase complex (Hda1C) preferentially deacetylates histones H3 and H2B, and functionally interacts with Tup[1] to repress transcription
To understand the exact function of Hda1C in more detail, the acetylation patterns of histones H3 and H4 were determined by chromatin immunoprecipitation (ChIP) assays using antibodies recognizing di-acetyl H3 (K9 and K14) and tetra-acetyl H4, respectively
To determine whether Hda1C differentially affects histone acetylation depending on the transcriptional status of GAL genes, chromatin was prepared from wild-type and hda1Δ cells grown in medium containing glucose or galactose
Summary
Hda[1] histone deacetylase complex (Hda1C) preferentially deacetylates histones H3 and H2B, and functionally interacts with Tup[1] to repress transcription. We find that Hda1C binds to hyperactive genes, likely via the interaction between the Arb[2] domain of Hda[1] and RNA polymerase II. We report that Hda1C deacetylates H4, but not H3, at hyperactive genes to partially inhibit elongation. This role is contrast to that of the Set2–Rpd3S pathway deacetylating histones at infrequently transcribed genes. Histone acetylation/deacetylation within coding regions affects RNA Pol II elongation, transcription initiation from cryptic promoters, and histone exchange[2]. H3K4me[3] at promoter regions acts as a binding site for multiple HATs and HDACs3. The coiled-coil domains of Hda[2] and
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