Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq of bovine cells (MDBK) to study butyrate-induced histone modification

ABSTRACT: Utilizing next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3, H4 Cells were treated with 10 mM butyrate for 24 hr, The cells were scraped from the flask and homogenized with ice-cold Dounce homogenizer to release the nuclei. The collected nuclei were resuspended in digestion buffer and enzymatic shearing was performed. ChIP with anti H3, H4 and acetyl-H3 and acetyl-H4.

ORGANISM(S): Bos taurus

SUBMITTER: Congjun Li

PROVIDER: E-GEOD-38973 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Structure of the Hir histone chaperone complex

Project description:The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1/Asf1 co-chaperone cooperate for replication-independent chromatin assembly. Here we report the molecular architecture of the Hir complex with Asf1/H3/H4 via single-particle cryo-EM and crosslinking mass spectrometry.

2024-08-22 | PXD040705 | Pride

ChIP-seq of bovine cells (MDBK) to study butyrate-induced histone modification

Project description:Utilizing next-generation sequencing technology, combined with ChIP (Chromatin Immunoprecipitation) technology to analyze histone modification (acetylation) induced by butyrate and to map the epigenomic landscape of normal histone H3, H4

2014-01-24 | GSE38973 | GEO

Global and specific responses of the histone acetylome to systematic perturbation

Project description:Regulation of histone acetylation is fundamental to the utilisation of eukaryotic genomes in chromatin. Aberrant acetylation contributes to disease and can be clinically combated by inhibiting the responsible enzymes. Our knowledge of the histone acetylation system is patchy because we so far lacked the methodology to describe acetylation patterns and their genesis by integrated enzyme activities. We devised a generally applicable, mass spectrometry-based strategy to precisely and accurately quantify combinatorial modification motifs. This was applied to generate a comprehensive inventory of acetylation motifs on histones H3 and H4 in Drosophila cells. Systematic depletion of known or suspected acetyltransferases and deacetylases revealed specific alterations of histone acetylation signatures, established enzyme-substrate relationships and unveiled an extensive crosstalk between neighboring modifications. Unexpectedly, overall histone acetylation levels remained remarkably constant upon depletion of individual acetyltransferases. Conceivably, the acetylation level is adjusted to maintain the global charge neutralisation of chromatin and the stability of nuclei.

2015-01-09 | PXD001394 | Pride

Proteomics analysis of ligated and recombinant human histones H3 and H4

Project description:A library of unmodified and differentially modified human histones H3 and H4 was prepared using native chemical ligation as described previously (Bartke et al., 2010; Nakamura et al., 2019). The modification status of histone H3 and H4 products was confirmed by LC-MS/MS.

2023-12-10 | PXD020773 | Pride

Gene expression changes upon the mutation of individual residues of histone H3 and H4

Project description:Nucleosome structure directly influences gene transcription. However, the function of each histone residue remains largely unknown. Here we profiled gene expression changes upon the mutation of individual residues of histone H3 and H4. Histone residues grouped by expression change similarity displayed overall structural relevance. This regulatory functional map of the core histones led to novel findings. First, the residues specific to each histone family tend to be more influential than those commonly found among different histones. Second, unlike histone acetylations, H3K4 trimethylation does not appear to be prerequisite for gene activation. Third, H3Q5 has been newly identified for its putative interactions with many chromatin regulators for transcription control. Lastly, the nucleosome lateral surface seems to play a key role through interactions with the surrounding DNA. Remarkably, we discovered a novel role for H3K56 in chromatin dynamics. The deletion of this residue, but not the alteration of acetylation states, caused a genome-wide decrease in nucleosome mobility and stabilized nucleosome positioning near transcription start and end sites. Occupying the DNA entry/exit site, H3K56 is thought to modulate nucleosome sliding along DNA. Taken together, genomics approaches such as microarray and deep sequencing prove valuable for mapping the function of histone residues. Microarray analysis was performed for 123 histone mutants and four wild-types as two reaplications of H3 and H4 of Saccharomyces ceravisiae.

2012-12-05 | E-GEOD-29059 | biostudies-arrayexpress

Gcn5 and Esa1 function as histone crotonyltransferases to regulate crotonylation-dependent transcription

Project description:Histone post-translational modifications (PTMs) are critical for processes such as transcription. The more notable among these are the non-acetyl histone lysine acylation modifications such as crotonylation, butyrylation and succinylation. However, the biological relevance of these PTMs is not fully understood because their regulation is largely unknown. Here, we set out to investigate whether the main histone acetyltransferases in budding yeast, Gcn5 and Esa1, possess crotonyltransferase activity. In vitro studies revealed that the Gcn5-Ada2-Ada3 (ADA) and Esa1-Yng2-Epl1 (Piccolo NuA4) histone acetyltransferase complexes have the capacity to crotonylate histones. Mass spectrometry analysis revealed that ADA and Piccolo NuA4 crotonylate lysines in the N-terminal tails of histone H3 and H4, respectively. Functionally, we show that crotonylation selectively affects gene transcription in vivo in a manner dependent on Gcn5 and Esa1. Thus, we identify the Gcn5- and Esa1-containing ADA and Piccolo NuA4 complexes as bona fide crotonyltransferases that promote crotonylation-dependent transcription.

2019-11-06 | PXD015488 | Pride

Quantification of histone H3 and H4 modifications by mass spectrometry in wildtype and MCM2-2A mutants of mice ESCs

Project description:During DNA replication modified parental histones H3-H4 are segregated almost symmetrically to the two daughter DNA strands enabling mitotic inheritance of histone PTMs. Whether heritable histone modifications confer epigenetic regulation by maintaining chromatin states and gene expression is unclear. Using MCM2 histone-binding mutant embryonic stem cells (ESCs) and mass spectrometry, we show that asymmetric segregation of parental histones to the leading strand causes imbalanced inheritance of histone H3K27 methylations to daughter cells.

2023-08-30 | PXD020326 | Pride

Acetyl-H4 chIP-seq of control, NaBu-treated, and random behavioral clusters of zebrafish 8 dpf larvae

Project description:We wanted to analyze the differences in acetyl-H4 content related to inter-individual behavioral variability. We retrieved three groups of samples: The first one was composed by 4 different clusters of zebrafish composed each one by 5 zebrafish larvae. Within each cluster, the behavioral differences across the larvae were minimal, while between the clusters, there were high differences in the behavior. The second one was composed by 4 different clusters of sodium butyrate (NaBu)-treated zebrafish composed each one by 5 larvae. The selection choice was the same as in the first group, but due to their behavioral effect of NaBu, the differences between the clusters were significantly reduced compared to control. The third one was composed by 3 different clusters of 5 zebrafish each randomly selected from the behavioral space. This group is a control of variability not associated to behavior.

2017-09-01 | E-MTAB-5993 | biostudies-arrayexpress

Protein kinase C coordinates histone H3 phosphorylation and acetylation

Project description:The re-assembly of chromatin following DNA replication is a critical event in the maintenance of genome integrity. Histone H3 acetylation at K56 and phosphorylation at T45 are two important chromatin modifications that accompany chromatin assembly. Here we report a microarray expression study of the protein kinase Pkc1, histone acetyl transferase Rtt109 and histone H3 in Saccharomyces cerevisiae under conditions of replicative stress.

2015-12-04 | E-MTAB-3359 | biostudies-arrayexpress

Genome-Wide Promoter Analysis of Epigenetic Regulation by Cocaine (MM5 data)

Project description:Changes in gene expression contribute to the long-lasting regulation of the brain's reward circuitry seen in drug addiction, however, the specific genes regulated and the transcriptional mechanisms underlying such regulation remain poorly understood. Here, we used chromatin immunoprecipitation coupled with promoter microarray analysis to characterize genome-wide epigenetic changes in the mouse nucleus accumbens, a crucial brain reward region, after repeated cocaine administration. Our findings reveal several interesting principles of gene regulation by cocaine and of the role of Î?FosB and CREB, two prominent cocaine-induced transcription factors, in this brain region. Mice were treated with cocaine or saline. Chromatin immunoprecipitation was performed for acetylated histone H3 and H4 as described previously (Kumar et al., 2005) with minor modifications. Immunoprecipitated DNA was amplified via ligation-mediated PCR and hybridized to Nimblgen mouse MM5 promoter arrays. 2 biological replicates per condition.

2010-05-18 | E-GEOD-16183 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data