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Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast (ChIP-seq)

ABSTRACT: Hda1C directly binds to actively transcribed regions likely via the interaction with elongating RNA PolII and/or with nascent RNA transcripts. The Arb2 domain of Hda1 is also critical for its binding to chromatin. Interestingly, Hda1C specifically deacetylates histone H4 but not H3 at active genes to suppress nucleosome instability and partially inhibit elongation. In contrast, Hda1C mainly deacetylates histone H3 at inactive genes to delay gene induction.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE121761 | GEO | 2019/07/22

REPOSITORIES: GEO

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Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast (RNA-seq)

Project description:Hda1C directly binds to actively transcribed regions likely via the interaction with elongating RNA PolII and/or with nascent RNA transcripts. The Arb2 domain of Hda1 is also critical for its binding to chromatin. Interestingly, Hda1C specifically deacetylates histone H4 but not H3 at active genes to suppress nucleosome instability and partially inhibit elongation. In contrast, Hda1C mainly deacetylates histone H3 at inactive genes to delay gene induction.

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Control pull-downs testing the effect of histone native chemical ligation on protein binding to di-nucleosomes

Project description:Here we examined whether histones H3 and H4 produced using native chemical ligation reaction affect protein binding to di-nucleosomes. To test this we performed a set of affinity purification pull-downs using di-nucleosomes containing the following histones H3 and H4: 1. ligated unmodified histone H3 and recombinant wild type histone H4 (unmod. H3), 2. recombinant wild type histone H3 and ligated unmodified histone H4 (unmod. H4) 3. ligated unmodified histones H3 and H4 (unmod. H3&H4). 4. recombinant wild type histones H3 and H4 (WT) Each pull-down was performed in three replicates. Co-purified proteins were quantified using label-free MS. Note that ligated histones H3 and H4 contain T32C or I29C single amino acid substitutions, respectively, that are introduced by the native chemical ligation procedure. In addition, ligated histone H4 is N-terminally acetylated to mimic its naturally blocked N-terminus.

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Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast.

Project description: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.

| S-EPMC6753149 | biostudies-literature

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