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Histone H3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells

ABSTRACT: Lysine 56 acetylation in the helical core of histone H3 opens yeast chromatin and enables histone gene transcription, DNA replication, DNA repair, and prevents epigenetic silencing. While K56Ac is globally abundant in yeast and flies its presence has been uncertain in mammals. We show here using mass spectrometry and genome wide analyses that K56Ac is present in human embryonic stem cells (hESCs) overlapping strongly at active and inactive promoters with the binding of the key regulators of pluripotency NANOG, SOX2 and OCT4. This includes also the canonical histone gene promoters and those for the hESC-specific microRNAs. K56Ac then relocates to developmental genes upon cellular differentiation. Thus K56Ac state more accurately reflects the epigenetic differences between hESCs and somatic cells than other active histone marks such as H3 K4 tri-methylation and K9 acetylation. These results suggest that K56Ac is involved in the human core transcriptional network of pluripotency.

ORGANISM(S): Homo sapiens

PROVIDER: GSE14749 | GEO | 2009/02/10

SECONDARY ACCESSION(S): PRJNA112237

REPOSITORIES: GEO

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Histone H3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells

Project description:Lysine 56 acetylation in the helical core of histone H3 opens yeast chromatin and enables histone gene transcription, DNA replication, DNA repair, and prevents epigenetic silencing. While K56Ac is globally abundant in yeast and flies its presence has been uncertain in mammals. We show here using mass spectrometry and genome wide analyses that K56Ac is present in human embryonic stem cells (hESCs) overlapping strongly at active and inactive promoters with the binding of the key regulators of pluripotency NANOG, SOX2 and OCT4. This includes also the canonical histone gene promoters and those for the hESC-specific microRNAs. K56Ac then relocates to developmental genes upon cellular differentiation. Thus K56Ac state more accurately reflects the epigenetic differences between hESCs and somatic cells than other active histone marks such as H3 K4 tri-methylation and K9 acetylation. These results suggest that K56Ac is involved in the human core transcriptional network of pluripotency. Genome wide location analysis ChIP-chip was performed in two human embryonic stem cell lines (HSF1 and HSF6) and two somatic cell lines (ARPE and BJ), for each of the following histone modifications: H3 K56Ac, H3 K9Ac, H3 K4me3 and H3 K27me3.

2009-02-09 | E-GEOD-14749 | biostudies-arrayexpress

Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis

Project description:The histone variant H2A.Z is a hallmark of nucleosomes flanking the promoters of protein coding genes, and is often found in nucleosomes that also carry lysine 56- acetylated histone H3 (H3-K56Ac), a mark which promotes rapid replication- independent turnover of nucleosomes. Although H2A.Z and H3-K56Ac have been generally implicated in transcriptional activation, their exact contributions have remained elusive. Here we find that H3-K56Ac promotes RNA polymerase II occupancy at a large number of protein coding and noncoding loci, yet neither H3- K56Ac nor H2A.Z has a significant impact on steady state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on levels of both coding and noncoding RNAs (ncRNAs) are only revealed in the absence of the nuclear RNA exosome. H2A.Z is also necessary for expression of divergent, promoter-proximal ncRNAs in mouse embryonic stem cells, suggesting a conserved role for H2A.Z across eukaryotes. Finally, we show that H2A.Z functions with H3-K56Ac in chromosome folding, facilitating formation of chromosome interaction domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher order chromatin structures.

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Genome-wide profiling of total RNA from mutants that affect chromatin dynamics: RTT109, SWR1, and the nuclear RNA exosome RRP6

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Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis (ChIP-seq)

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Chromatin dynamics and the RNA exosome function in concert to regulate transcriptional homeostasis (ChIP-seq)

2015-11-12 | E-GEOD-72692 | biostudies-arrayexpress

Isw1 and Chd1 maintain chromatin organization during transcription [K56ac data]

Project description:ChIP-chip assays to determine the occupancy of acetylated histone H3 K56 in wildtype, isw1, chd1, isw1 chd1 and ISW1[K227R] yeast. Two color experiment. ChIP/Input. K56ac data normalized to histone H3 and plotted as mutant over wildtype. Biological replicates=3. Please note that H3 data for YMS123-125 & YMS127 is part of the AcH4 file.

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A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme

Project description:The histone variant H2A.Z plays key roles in gene expression, DNA repair, and centromere function. H2A.Z deposition is controlled by SWR-C chromatin remodeling enzymes that catalyze the nucleosomal exchange of canonical H2A with H2A.Z. Here we report that acetylation of histone H3 lysine 56 (H3-K56Ac) alters the substrate specificity of SWR-C, leading to promiscuous dimer exchange where either H2A.Z or H2A can be exchanged from nucleosomes. This result is confirmed in vivo, where genome-wide analysis demonstrates widespread decreases in H2A.Z levels in yeast mutants with hyperacetylated H3K56. Our work also suggests that a conserved SWR-C subunit may function as a M-bM-^@M-^\lockM-bM-^@M-^] that prevents removal of H2A.Z from nucleosomes. Our study identifies a histone modification that regulates a chromatin remodeling reaction and provides insights into how histone variants and nucleosome turnover can be controlled by chromatin regulators. H2A.Z ChIP seq experiments in mutants with constitutive H3K56ac

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A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme

Project description:The histone variant H2A.Z plays key roles in gene expression, DNA repair, and centromere function. H2A.Z deposition is controlled by SWR-C chromatin remodeling enzymes that catalyze the nucleosomal exchange of canonical H2A with H2A.Z. Here we report that acetylation of histone H3 lysine 56 (H3-K56Ac) alters the substrate specificity of SWR-C, leading to promiscuous dimer exchange where either H2A.Z or H2A can be exchanged from nucleosomes. This result is confirmed in vivo, where genome-wide analysis demonstrates widespread decreases in H2A.Z levels in yeast mutants with hyperacetylated H3K56. Our work also suggests that a conserved SWR-C subunit may function as a “lock” that prevents removal of H2A.Z from nucleosomes. Our study identifies a histone modification that regulates a chromatin remodeling reaction and provides insights into how histone variants and nucleosome turnover can be controlled by chromatin regulators.

2013-04-15 | GSE43935 | GEO

LncPRESS1 is a p53-regulated lncRNA that safeguards pluripotency by disrupting SIRT6 mediated de-acetylation of histone H3K56

Project description:Recent evidence suggests that lncRNAs play an integral regulatory role in numerous functions, including determination of cellular identity. We determined global expression (RNA-seq) and genome wide profiles (ChIP-seq) of histone post-translational modifications and p53 binding in human embryonic stem cells (hESCs) undergoing differentiation to define a high-confidence set of 40 lncRNAs, which are p53 transcriptional targets. We focused on lncRNAs, highly expressed in pluripotent hESCs and repressed by p53 during differentiation, to identify lncPRESS1 as a p53-regulated transcript that maintains hESC pluripotency in concert with core pluripotency factors. RNA-seq of hESCs depleted of lncPRESS1 revealed that lncPRESS1 controls a gene network that promotes pluripotency. Further, we found that lncPRESS1 physically interacts with SIRT6 to prevent SIRT6 chromatin localization and maintain high levels of histone H3K56 and H3K9 acetylation at promoters of pluripotency genes. In summary, we describe a novel pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity

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Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange

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