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Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [Cut & Tag]

ABSTRACT: Tip60-dependnet histone modification/occupancy dynamics during Ascl1-mediated direct reprogramming of mouse embryonic fibroblasts (MEFs) into induced neuronal cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE181888 | GEO | 2022/11/22

REPOSITORIES: GEO

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Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [ATAC-Seq]

Project description:Examination of the effects of Tip60/Kat5 depletion on chromatin accessibility dynamics during Ascl1-mediated direct reprogramming of mouse embryonic fibroblasts (MEFs) into induced neuronal cells.

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Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [RNA-Seq]

Project description:Examination of the effects of Tip60/Kat5 depletion on gene expression dynamics during Ascl1-mediated direct reprogramming of mouse embryonic fibroblasts (MEFs) into induced neuronal cells.

2022-11-22 | GSE181887 | GEO

Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [Cut & Tag]

Project description:Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [Cut & Tag]

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Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation.

Project description:Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation.

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Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation.

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

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Detection of H2AZ acetylation, total H2AZ, and H4K8 and H4K16 acetylation by CUT&Tag-sequencing

Project description:In this study we examined the effects of loss of the MYST histone acetyltransferase TIP60 (KAT5) in mouse embryonic fibroblasts (MEFs), human embryonic kidney cells 293 (HEK293), and human osteosarcoma cells (U2OS) on cell proliferation, BrdU incorporation, cell cycle progression, apoptotic and other forms of cell death, DNA damage, histone acetylation at specific lysine residues and RNA expression levels. This dataset relates to U2OS cells. CUT&Tag was performed on replicate cultures and 100,000 cells per sample, 43,000 human cells each of U2OS with inducible single guide RNA #1 (g1/C9) or inducible single guide RNA #2 (g2/C9) expression and both with constitutive expression of Cas9 enzyme, either treated with doxycycline for 4 days (KO) or untreated (CTL) and 57,000 D. melanogaster cells as a spike-in, in total two replicates of TIP60 deleted cells and two replicates of control cells.

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RNA-sequencing data of Tip60 deleted and control mouse embryonic fibrobasts

Project description:In this study we examined the effects of loss of the MYST histone acetyltransferase TIP60 (KAT5) in mouse embryonic fibroblasts (MEFs), human embryonic kidney cells 293 (HEK293), and human osteosarcoma cells (U2OS) on cell proliferation, BrdU incorporation, cell cycle progression, apoptotic and other forms of cell death, DNA damage, histone acetylation at specific lysine residues and RNA expression levels. This dataset relates to MEFs. To assess the effects of loss of TIP60 on RNA levels, RNA-seq was performed on MEFs, where the TIP60 gene was deleted using Cre/loxP technology. Nuclear translocation was induced with 4-OH-tamoxifen treatment for 3 and 5 days to induce TIP60 gene deletion in the samples also containing the loxP sited in the Tip60 locus.

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Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [ATAC-Seq]

Project description:Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [ATAC-Seq]

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Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [RNA-Seq]

Project description:Tip60-mediated H2A.Z acetylation is required for neuronal fate specification and bivalent gene activation [RNA-Seq]

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JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions.

Project description:Histone variants differ in amino acid sequence, expression timing and genomic localization sites from canonical histones and convey unique functions to eukaryotic cells. Their tightly controlled spatial and temporal deposition into specific chromatin regions is accomplished by dedicated chaperone and/or remodeling complexes. While quantitatively identifying the chaperone complexes of many human H2A variants by using mass spectrometry, we also found additional members of the known H2A.Z chaperone complexes p400/TIP60/NuA4 and SRCAP. We discovered JAZF1, a nuclear/nucleolar protein, as a member of a p400 sub-complex containing MBTD1 but excluding ANP32E. Depletion of JAZF1 results in transcriptome changes that affect, among other pathways, ribosome biogenesis. To identify the underlying molecular mechanism contributing to JAZF1's function in gene regulation, we performed genome-wide ChIP-seq analyses. Interestingly, depletion of JAZF1 leads to reduced H2A.Z acetylation levels at > 1000 regulatory sites without affecting H2A.Z nucleosome positioning. Since JAZF1 associates with the histone acetyltransferase TIP60, whose depletion causes a correlated H2A.Z deacetylation of several JAZF1-targeted enhancer regions, we speculate that JAZF1 acts as chromatin modulator by recruiting TIP60's enzymatic activity. Altogether, this study uncovers JAZF1 as a member of a TIP60-containing p400 chaperone complex orchestrating H2A.Z acetylation at regulatory regions controlling the expression of genes, many of which are involved in ribosome biogenesis.

| S-EPMC7826843 | biostudies-literature

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