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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE208378 | GEO | 2022/07/22

REPOSITORIES: GEO

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RNA-sequencing data of TIP60 mutated and control U2OS cells

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. To assess the effects of loss of TIP60 on RNA levels, RNA-seq was performed on U2OS cells, where the TIP60 gene was mutated by CRISPR/Cas9 technology using single guide RNA #1 (g1/C9), single guide RNA #2 (g2/C9), or guide-only controls (g1 or g2). The expression of the guide RNA was induced with doxycycline treatment for 4 days to induce TIP60 gene mutation in the samples also expressing the Cas9 enzyme.

2022-07-22 | GSE208382 | GEO

RNA-sequencing data of TIP60 mutated and control HEK293 cells

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 HEK293 cells. To assess the effects of loss of TIP60 on RNA levels, RNA-seq was performed on HEK293 cells, where the TIP60 gene was mutated by CRISPR/Cas9 technology using single guide RNA #1 (g1/C9), single guide RNA #2 (g2/C9), or guide-only controls (g1 or g2). The expression of the guide RNA was induced with doxycycline treatment for 3 days to induce TIP60 gene mutation in the samples also expressing the Cas9 enzyme.

2022-07-22 | GSE208379 | GEO

TIP60-dependent acetylation on H2AZ lysine 7 regulates the transcriptional program for genome stability [RNA-seq]

Project description:TIP60 mediated acetylation of H2AZ on gene promoter results in change in transcriptional landscape, and further regulates expression of genes involved in the maintenance of genome stability.

2019-12-01 | GSE110406 | GEO

TIP60-dependent acetylation on H2AZ lysine 7 regulates the transcriptional program for genome stability [ChIP-seq]

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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.

2022-07-22 | GSE208380 | GEO

TIP60-dependent acetylation on H2AZ lysine 7 regulates the transcriptional program for genome stability

Project description:TIP60-dependent acetylation on H2AZ lysine 7 regulates the transcriptional program for genome stability

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MRG proteins are shared by multiple protein complexes with distinct functions.

Project description:In this study, we characterized MORF4L1/MRG15 interactome. Using Flag-ChIP-sequencin K562 cells, we first claimed that both MRG15 isoforms (long or short chromodomain) and MORF4L2/MRGX which does not contain any chromodomain, shared mostly the same targets. Then, we described a new factor associated to MRG15, called EP400NL. EP400NL binds to BRD8 also linked to MRGBP and MRG15/X to form a new complex homolog to the yeast TINTIN. Using RNA-sequencing in BRD8 or MRGBP or MRG15/MRGX and KAT5/TIP60-depleted U2OS cells, we observed that human TINTIN plays a role in gene expression regulation independently of NuA4/TIP60 complex.

2021-08-17 | GSE181533 | GEO

Histone acetylation dependent microarray analysis uncovers a role for Tip60 HAT activity in nervous system function and general metabolism

Project description:Tip60 is a key histone acetyltransferase (HAT) enzyme that plays a central role in diverse biological processes critical for general cell function, however the chromatin-mediated cell-type specific developmental pathways that are dependent exclusively upon the HAT activity of Tip60 remain to be explored. Here, we investigate the role of Tip60 HAT activity in transcriptional control during multicellular development, in vivo by examining genome-wide changes in gene expression in a Drosophila model system specifically depleted for endogenous dTip60 HAT function. We show that amino acid residue E431 in the catalytic HAT domain of dTip60 is critical for the acetylation of endogenous histone H4 in our fly model in vivo, and demonstrate that dTip60 HAT activity is essential for multicellular development. Moreover, our results uncover a novel role for Tip60 HAT activity in controlling neuronal specific gene expression profiles essential for nervous system function as well as a central regulatory role for Tip60 HAT function in general metabolism. Drosophila larvae ubiquitously expressing either our dTIP60 HAT specific mutant or an additional copy of wild type dTIP60 were selected along with age-matched wild type controls for RNA extraction. Two samples, each containing a pool of thirty-five staged whole larvae, were collected from each respective genotypic cross, and were used for hybridization on a separate Affymetrix microarray.

2010-11-29 | E-GEOD-25635 | biostudies-arrayexpress

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

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

2022-11-22 | GSE181888 | GEO

Hdac6 is a stem-cell specific modulator of Tip60-p400 function (gene expression)

Project description:To identify the functional role of Hdac6 in embryonic stem cells, we examined gene expression changes in mouse ES cells upon Tip60, Hdac6 and double knockdown. Two biological replicates each for control (GFP), Tip60, Hdac6 and double KD in E14 mouse ESCs. Lentiviral-based shRNA was used and gene expression changes were determined 3 days after KD. The global gene expression profiles of Tip60, Hdac6 and double KD were compared to control KD cells.

2013-11-20 | E-GEOD-42208 | biostudies-arrayexpress

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