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ChIP-seq of MYST acetyltransferases in RKO cell line

ABSTRACT: Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells. Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells.

ORGANISM(S): Homo sapiens

SUBMITTER: Eric Paquet

PROVIDER: E-GEOD-63722 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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BRPF3-HBO1 regulates replication origin activation and histone H3K14 acetylation.

Feng Yunpeng Y Vlassis Arsenios A Roques Céline C Lalonde Marie-Eve ME González-Aguilera Cristina C Lambert Jean-Philippe JP Lee Sung-Bau SB Zhao Xiaobei X Alabert Constance C Johansen Jens V JV Paquet Eric E Yang Xiang-Jiao XJ Gingras Anne-Claude AC Côté Jacques J Groth Anja A

The EMBO journal 20151130 2

During DNA replication, thousands of replication origins are activated across the genome. Chromatin architecture contributes to origin specification and usage, yet it remains unclear which chromatin features impact on DNA replication. Here, we perform a RNAi screen for chromatin regulators implicated in replication control by measuring RPA accumulation upon replication stress. We identify six factors required for normal rates of DNA replication and characterize a function of the bromodomain and ...[more]

PMID: 26620551

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ChIP-seq of MYST acetyltransferases in RKO cell line

Project description:Genome-wide mapping of MYST acetyltransferase subunit BRPF3 in RKO synchronised cells.

2016-02-05 | GSE63722 | GEO

Genome-wide map of HBO1 in cancer derived human cell line

Project description:We used ChIP-seq technology in order to map chromatin binding sites of the HBO1 MYST complex in the RKO cell line. We obtained a significant enrichment of the HBO1 signal right after TSS regions of genes and also In the proximal promoter region, with no signal on TSS. This enrichment also correlates with gene expression level. HBO1 signal in RKO cell line.

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ChIP-seq of MYST acetyltransferases

Project description:Histone acetyltransferases (HAT) assemble into multisubunit complexes in order to target distinct lysine residues on nucleosomal histones. Here, we characterize native HAT complexes assembled by the BRPF-family of scaffold proteins. Their PHD-ZnKnuckle-PHD domain is essential for binding chromatin and restricted to unmethylated H3K4, a specificity that is reversed by the associated ING subunit. Native BRPF1 complexes can contain either MOZ/MORF or HBO1 as catalytic acetyltransferase subunit. Interestingly, while the previously reported HBO1 complexes containing JADE scaffold proteins target histone H4, the HBO1-BRPF1 complex acetylates only H3 in chromatin. We mapped a small region at the N-terminus of scaffold proteins responsible for histone tail selection on chromatin. Thus, alternate choice of subunits associated with HBO1 can switch its specificity from H4 to H3 tails, highlighting a crucial new role of associated subunits within HAT complexes, previously thought to be intrinsic to the catalytic subunit. Genome-wide mapping of MYST acetyltransferases subunits and H3K4me3 histone mark in RKO cells.

2013-10-09 | E-GEOD-47190 | biostudies-arrayexpress

Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation

Project description:Analysis of histone acetyl transferases (HATs) from the MYST and GNAT families in S. pombe to identify functional differences or overlap with regard to gene expression. Mutations were made to Elp3 and Gcn5 (GNAT family), and to Mst2 (MYST family). Mutants showed distinct phenotypes which were repressed or enhanced by mutant combinations. This SuperSeries is composed of the following subset Series: GSE17259: S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation, dual-channel dataset GSE17262: S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation, Affymetrix dataset Refer to individual Series

2009-09-19 | E-GEOD-17298 | biostudies-arrayexpress

Limited-proteolysis coupled to mass spectrometry (LiP-MS) data on a serially filtered yeast lysate (the FLiP library) and on lysates of wild-type and Gcn5 mutant yeast strains grown under hydroxyurea stress and control conditions. Affinity purification mass spectrometry on Ada3 pulldowns from yeast grown under hydroxyurea stress and control conditions.

Project description:We applied serial ultrafiltration and limited proteolysis-coupled mass spectrometry (LiP-MS) to generate an atlas of peptides that act as markers for the formation or dissolution of protein-protein interactions (PPIs). Applied to Saccharomyces cerevisiae, the approach yielded 6,441 candidate PPI markers from 1,086 proteins, including 1,072 markers of known interfaces from 272 proteins. These include peptides mapping to both validated and putative protein binding interfaces, as well as markers of structural changes that accompany PPIs. The approach is based on detecting differences in protease susceptibility between the protein complex-bound and monomeric forms. We then used these peptide markers to track changes in protein-protein interactions in LiP-MS analyses of unfractionated lysates of yeast grown under hydroxyurea (HU) stress compared to control conditions. We captured known and novel protein complex rearrangements, supporting the key role played by Spt-Ada-Gcn5 acetyltransferase (SAGA) and the activity of its acetyltransferase Gcn5 in the stress response. We validated our observed rearrangement of SAGA with an AP-MS experiment comparing Ada3 pulldowns of yeast grown under HU and control conditions. We further examined how protein complex rearrangements change in Gcn5 mutant cells; we found a set of protein complexes that depend directly or indirectly on Gcn5 activity and identified a link between Gcn5 activity and the regulation of P-bodies.

2024-10-17 | PXD055566 | Pride

Homo sapiens

Project description:ChIP-seq of MYST acetyltransferases in RKO cell line

| PRJNA269250 | ENA

Genome-wide map of HBO1 in cancer derived human cell line

2012-03-15 | GSE33007 | GEO

PKC1 cell cycle study

Project description:Transcriptional profiling of a Saccharomyces cerevisiae protein kinase Pkc1p temperature sensitive mutant on cells synchronised in S phase and then released. The Mcm1p-Fkh2p-Ndd1p complex in Saccharomyces cerevisiae controls the cyclical expression of the CLB2 cluster of genes at the G2/M phase transition. The activity of this complex is known to be positively controlled by cyclin-CDK and polo kinases. The current experiment aimed to demonstrate that the protein kinase Pkc1p works in the opposite manner to inhibit the activity of the Mcm1p-Fkh2p-Ndd1p complex and the expression of its target genes.

2013-03-14 | E-MEXP-3667 | biostudies-arrayexpress

RNAi promotes heterochromatic silencing through replication-coupled release of RNA pol II (ChIP-seq)

Project description:Heterochromatin comprises tightly compacted repetitive regions of eukaryotic chromosomes. The inheritance of heterochromatin through mitosis requires RNA interference (RNAi), which guides histone modification 1 during the DNA replication phase of the cell cycle2. Here, we show that the alternating arrangement of origins of replication and non-coding RNA in pericentromeric heterochromatin results in competition between transcription and replication. Co-transcriptional RNAi releases RNA polymerase II (PolII), allowing completion of DNA replication by the leading strand DNA polymerase, and associated histone modifying enzymes3 which spread heterochromatin with the replication fork. In the absence of RNAi, stalled forks are repaired by homologous recombination without histone modification. RNA PolII ChIP from wild type and dcr1-deleted samples in exponentially growing and HU-arrested cultures.

2011-07-29 | E-GEOD-31016 | biostudies-arrayexpress

The effect of γ-butyrolactone (MB3) treatment on the transcript response after wounding of Arabidopsis thaliana roots

Project description:In a previous study, we found that wound-induced transcriptional expression is strongly correlated with an increase of the level of acetylation of the N-tails of histone 3. To investigate if the increase in histone acetylation is a prerequisite for the induction of wound-induced gene expression, we performed transcriptional profiling of wounded roots with and without treatment with γ-butyrolactone (MB3), a chemical inhibitor of GNAT-MYST family of histone acetyltransferase .

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