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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.

2019-07-22 | GSE121762 | GEO

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

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-07-22 | GSE121763 | GEO

Nutrient Starvation-induced Hda1C Rewiring: coordinated regulation of transcription and translation

Project description:In yeast, Hda1 histone deacetylase complex (Hda1C) plays an important role in transcriptional regulation by modulating histone acetylation. We here explored the dynamics of Hda1C binding in nutrient-rich and -starved conditions. Chromatin immunoprecipitation sequencing revealed that starvation alters RNA Pol II and Hda1C binding to coding genes in a highly correlated manner. Interestingly, we discovered RNA Pol II transcription-independent recruitment of Hda1C to intergenic regions, particularly the upstream regulatory sequences (URS) of ribosomal protein (RP) genes, which are enriched with Rap1 binding sites. Under nutrient starvation, Rap1 contributes to the recruitment of Hda1C to these URS regions, where Hda1C deacetylates histones, thereby fine-tuning basal gene expression and delaying RP gene reactivation. Furthermore, Hda1C is also required for RNA Pol I transcription of rRNAs and RNA Pol III transcription of tRNA genes, especially in nutrient-limited conditions. Significantly, Hda1C mutants are sensitive to translation inhibitors and display altered ribosome profiles. Thus, Hda1C may coordinate transcriptional regulation within the nucleus with translation control in the cytoplasm and could be a key regulator of gene expression responses to nutrient stress.

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

Project description:Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast

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Chromatin immunoprecipitation of wild type, SET2 deletion, Rco1 PHD domain deletion and Eaf3 chromodomain deletion yeast using anti-acetyl-histone H4

Project description:Nucleosomes must be deacetylated behind elongating RNA polymerase II to prevent cryptic initiation of transcription within the coding region. RNA polymerase II signals for deacetylation through methylation of histone H3 lysine 36 (H3K36) which provides the recruitment signal for the Rpd3S deacetylase complex. Recognition of methyl-H3K36 by Rpd3S requires the chromodomain of its Eaf3 subunit. Paradoxically, Eaf3 is also a subunit of the NuA4 acetyltransferase complex yet NuA4 does not recognize methyl H3K36 nucleosomes. We found that methyl H3K36 nucleosome recognition by Rpd3S also requires the PHD domain of its Rco1 subunit. Thus, the coupled chromo and PHD domains of Rpd3S specifies recognition of the methyl H3K36 mark; demonstrating the first combinatorial domain requirement within a protein complex to read a specific histone code.

2007-05-16 | E-TABM-260 | biostudies-arrayexpress

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

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

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

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

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The histone chaperone NASP maintains H3-H4 reservoirs in the early Drosophila embryo

Project description:Histones are essential for chromatin packaging and histone supply must be tightly regulated as excess histones are toxic. To drive the rapid cell cycles of the early embryo, however, excess histones are maternally deposited. Therefore, soluble histones must be buffered by histone chaperones but the chaperone necessary to stabilize soluble H3-H4 pools in the Drosophila embryo has yet to be identified. Here, we show that CG8223, the Drosophila ortholog of NASP, is a H3-H4-specific chaperone in the early embryo. NASP specifically binds to H3-H4 in the early embryo. We demonstrate that, while NASP is non-essential in Drosophila, NASP is maternal effect lethal gene. Embryos laid by NASP mutant mothers have a reduce rate of hatching and show defects in early embryogenesis. Critically, soluble H3-H4 pools are degraded in embryos laid by NASP mutant mothers. Our work identifies NASP as the critical H3-H4 histone chaperone in the Drosophila embryo.

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