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Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors reveals histone specific acetylation changes [ChIP-seq]

ABSTRACT: Histone deacetylases inhibitors (HDACi) have emerged as valuable therapeutics in cancer and other diseases, yet their effect on histone post-translational modification remains incompletely characterized. Here, we applied quantitative mass spectrometry and high throughput sequencing to systematically profile site-specific histone modification changes in response to a panel of HDAC inhibitors. This platform enabled mapping of histone modification changes across hundreds of sites including low abundant histone marks. Furthermore, integrative analysis of ChIP-seq and RNA-seq identified genome wide binding site for a low-abundant histone mark H2A.Z acetylation in HeLa cells and MDA-MB-231 breast cancer cells, highlighting the role of H2A.Z acetylation in regulating gene expression through various biological pathways and specific genes involved in tumor suppressor pathways. Our findings provide a functional resource for identification and quantification of epigenetic changes and transcriptional regulation of histone H2A.Z acetylation upon pharmacological perturbation

ORGANISM(S): Homo sapiens

PROVIDER: GSE308263 | GEO | 2026/03/18

REPOSITORIES: GEO

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Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors revelas histone specific acetylation chnages [RNA-seq]

Project description:Histone deacetylases inhibitors (HDACi) have emerged as valuable therapeutics in cancer and other diseases, yet their effect on histone post-translational modification remains incompletely characterized. Here, we applied quantitative mass spectrometry and high throughput sequencing to systematically profile site-specific histone modification changes in response to a panel of HDAC inhibitors. This platform enabled mapping of histone modification changes across hundreds of sites including low abundant histone marks. Furthermore, integrative analysis of ChIP-seq and RNA-seq identified genome wide binding site for a low-abundant histone mark H2A.Z acetylation in HeLa cells and MDA-MB-231 breast cancer cells, highlighting the role of H2A.Z acetylation in regulating gene expression through various biological pathways and specific genes involved in tumor suppressor pathways. Our findings provide a functional resource for identification and quantification of epigenetic changes and transcriptional regulation of histone H2A.Z acetylation upon pharmacological perturbation

2026-03-18 | GSE308262 | GEO

Identification of PWWP2A interactors using label-free quantitative affinity enrichment mass spectrometry

Project description:Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified PWWP2A, which tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays we show that distinct domains of PWWP2A moreover mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly H3K36me3-containing gene bodies. Additionally, PWWP2A bind to an MTA1-specific core NuRD (M1HR) complex solely consisting of MTA1, HDAC1 and RBBP4/7, excluding CHD and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as an ever more complex chromatin binding protein serving as adapter for M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels and likely fine-tuning the transcriptional balance.

2018-08-27 | PXD010424 | Pride

Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors reveals histone specific acetylation changes [ChIP-seq]

Project description:Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors reveals histone specific acetylation changes [ChIP-seq]

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H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

Project description:The histone variant H2A.Z has been implicated in nucleosome exchange, transcriptional activation and Polycomb repression. However, the relationships among these seemingly disparate functions remain obscure. We mapped H2A.Z genome-wide in mammalian ES cells and neural progenitors. H2A.Z is deposited promiscuously at promoters and enhancers, and correlates strongly with H3K4 methylation. Accordingly, H2A.Z is present at poised promoters with bivalent chromatin and at active promoters with H3K4 methylation, but is absent from stably repressed promoters that are specifically enriched for H3K27 trimethylation. We also characterized post-translational modification states of H2A.Z, including a novel species dually-modified by ubiquitination and acetylation that is enriched at bivalent chromatin. Our findings associate H2A.Z with functionally distinct genomic elements, and suggest that post-translational modifications may reconcile its contrasting locations and roles. Examination of histone variant, histone modifications and transcription machinery in 3 cell types

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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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Comprehensive mass spectrometry screening-derived atlas of HDAC inhibitors revelas histone specific acetylation chnages [RNA-seq]

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Histone acetyltransferase 2 links H4 acetylation, H2A.Z deposition and transcription start site-choice in African trypanosomes

Project description:Both, acetylation of histones and of histone variant H2A.Z are conserved features of eukaryotic transcription start sites (TSSs) and both features appear to be critical for correct transcription initiation. However, complex patterns of transcriptional regulation have complicated the establishment of functional links between histone acetylation, H2A.Z deposition and their importance in transcription regulation. To elucidate these links, we took advantage of the unusual genome organization in Trypanosoma brucei, a highly divergent eukaryote. In T. brucei genes are organized in long polycistronic transcription units, drastically reducing the sites of transcription initiation. Employing a highly sensitive and quantitative mass-spectrometry-based approach, we quantified the genome-wide histone acetylation and methylation pattern and identified various acetyl and methyl marks exclusively enriched at TSSs In addition, we show that deletion of histone acetyltransferase 2 results in a loss of H4 acetylation at TSSs, a loss of H2A.Z deposition at TSSs and a shift in the sites of transcription initiation. Combined, our findings demonstrate an evolutionary conserved link between histone H4 acetylation, H2A.Z deposition and RNA transcription initiation.

2020-03-24 | PXD014452 | Pride

GCN5-mediated histone H3 Acetylation Orchestrates Gene Expression and Plant Development via H2A.Z

Project description:H2A.Z is a conserved histone variant that plays essential roles in various DNA-templated processes across eukaryotes. H2A.Z and histone post-translational modifications (PTMs) exert a bidirectional and context-dependent influence on each other. Nevertheless, the functions of the interplay between PTMs and H2A.Z level and the underlying molecular mechanism remain poorly understood. Here, we found that the loss of the histone acetyltransferase GCN5 impedes the overexpression of BSU1 typically observed in nrp1-1 nrp2-2, accompanied by changes in H3 acetylation and H2A.Z levels. Interestingly, the increment in H2A.Z levels typical of nrp1-1 nrp2-2 mutant alleviates the morphological and molecular phenotypes of gcn5. Conversely, H2A.Z-depleted mutants aggravate the phenotype of gcn5. In the gcn5 mutant, the H2A.Z level is globally reduced in the gene bodies, and this reduction is dependent on the histone chaperones NRP1 and NRP2. Additionally, the reduction of H3 acetylation levels caused by GCN5 depletion can be recovered in the nrp1-1 nrp2-2 mutant background, likely due to the over-accumulation of H2A.Z. In conclusion, our genetic, molecular, and genomic findings demonstrate that GCN5-mediated H3 acetylation promotes H2A.Z deposition, H2A.Z over-accumulation recovers the loss of GCN5-mediated H3 acetylation, and this interplay is crucial for regulating gene expression and plant development.

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H3 Acetylation and H2A.Z Levels Interplay to Regulate Gene Expression and Plant Development [RNA-seq]

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Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, mouse, ChIP-seq]

Project description:HDAC inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action, however, little is known of the extent of genome-wide changes of the mammalian genome when stimulated by the hydroxamic acids, TSA and SAHA. In primary human vascular endothelial cells we map the chromatin modifications, histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation mediated gene expression is often associated with modification of other lysine residues we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). Genome-wide mRNA sequencing indicates the differential expression of about 30% of genes, with almost equal numbers being up- and down- regulated. We observe deacetylation conferred by TSA and SAHA that are associated with decreased gene expression. Histone deacetylation is associated with the loss of p300/CBP binding at gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation. Mouse ChIP-seq profiles for histone acetylation treated and control samples were generated by deep sequencing, using Illumina GAIIx.

2014-02-23 | E-GEOD-54910 | biostudies-arrayexpress

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