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HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation [RNA-seq]

ABSTRACT: HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation [RNA-seq]

PROVIDER: PRJNA979181 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24806853_1.fastq.gz	Fastqsanger.gz
	SRR24806853_2.fastq.gz	Fastqsanger.gz
	SRR24806854_1.fastq.gz	Fastqsanger.gz
	SRR24806854_2.fastq.gz	Fastqsanger.gz
	SRR24806855_1.fastq.gz	Fastqsanger.gz

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HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation

Project description:HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation

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HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation [ChIP-seq]

Project description:HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation [ChIP-seq]

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HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation [RNA-seq]

Project description:Lysine succinylation is one of the major post-translational modifications occurred on histones and is believed to have significant roles in regulation of chromatin structure and function. Currently, histone desuccinylation is widely believed to be exerted by the members of SIRT family deacetylases. Here, we report that histone desuccinylation is in fact primarily catalyzed by the class I HDAC1/2/3. Inhibition or depletion of HDAC1/2/3 resulted in marked increase of global histone succinylation, whereas ectopic expression of HDAC1/2/3 but not their deacetylase inactive mutants downregulated global histone succinylation. We demonstrated that the class I HDAC1/2/3 complexes have robust histone desuccinylase activity in vitro. Genomic landscape analysis revealed that histone succinylation is highly enriched at gene promoters and inhibition of HDAC activity results in marked elevation of promoter histone succinylation. Furthermore, integrated analysis revealed that the promoter histone succinylation positively correlates with the transcriptional activity. Collectively, we demonstrate that the class I HDAC1/2/3 but not the SIRT family proteins are the major histone desuccinylases particularly important for promoter histone desuccinylation. Our study thus sheds new light on the role of histone succinylation in transcriptional regulation.

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HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation [ChIP-seq]

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Transcription profiling of embryonic stem cells from wild type and histone deacetylase 1 (HDAC1) knock out mice to identify putative HDAC1 target genes.

Project description:Histone deacetylase 1 (HDAC1) is an enzyme that promotes deacetylation of acetylated lysine residues in histones and other proteins. Histone acetylation is often associated with gene activation and expression. Los of HDAC1 leads to severe problems in development and proliferation. Moreover, it seems to be the major histone deacetylase in mouse embryonic stem cells. We used microarrays to identify putative HDAC1 target genes. Experiment Overall Design: Wild type and HDAC1 mouse embryonic stem cell, originating from same litter, were used for RNA extraction and hybridization on Affymetrix microarrays.

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HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation

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

2023-07-02 | GSE234006 | GEO

Rapid degradation of Histone Deacetylase 1 (HDAC1) reveals essential roles in both gene repression and active transcription

Project description:Histone Deacetylase 1 (HDAC1) removes acetyl groups from lysine residues on the core histones, balancing histone acetyltransferase (HAT) activity. Despite this apparent repressive function, suppression of HDAC activity causes both up and downregulation of gene expression. Here we exploit the degradation tag (dTAG) system to rapidly degrade HDAC1 in embryonic stem cells (ESCs) lacking the paralog, HDAC2. Unlike HDAC inhibitors that lack isoform specificity the dTAG system allowed specific HDAC1 targeting and completely removed HDAC1 100x faster than genetic knockouts. HDAC1 degradation caused rapid increases in histone acetylation, with H2BK5 and H2BK11 most sensitive. The majority of differentially expressed genes following 2 hours of HDAC1 degradation were upregulated (275 genes up vs 15 down) with increased proportions of downregulated genes at 6 (1153 up vs 443 down) and 24 hours (1146 up vs 967 down). Upregulated genes showed increased H2BK5ac and H3K27ac around their transcriptional start site (TSS). In contrast, decreased acetylation of super-enhancers (SEs) was linked to the most strongly downregulated genes, leading to a collapse of the core pluripotency-associated gene network. These findings suggest that HDAC1 plays a crucial role in regulating the ESC gene expression network by maintaining the correct acetylation levels at key genomic sites.

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Project description:We characterize histone crotonylation in intestinal epithelium-derived cells through Mass spectrometry, ChIp-Seq and RNA-Seq approaches and show that this modification is removed by class I histone deacetylases, HDAC1, 2 and 3.

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Class I histone deacetylases HDAC1, 2 and 3 are histone decrotonylases

Project description:Class I histone deacetylases HDAC1, 2 and 3 are histone decrotonylases

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