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The Genome Wide Distribution of Acetylated Histone H4 Remodelled through Human Primary Myoblast Differentiation

ABSTRACT: The simultaneous genotyping of tens of thousands of SNP using SNP microarrays is a very important tool that is revolutionizing genetics and molecular biology. In this work, we present a new application of this technique by using it to assess chromatin immunoprecipitation (CHIP) as a means to assess the multiple genomic locations bound by a protein complex recognized by an antibody. We illustrate the use of this technique with an analysis of the change in histone H4 acetylation, a marker of open chromatin and transcriptionally active genomic regions, which occur during the differentiation of human myoblasts into myotubes. Our results are validated by the observation of a significant correlation between the histone modifications detected and the expression of the nearby genes, as measured by DNA microarrays. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE4133 | GEO | 2006/08/28

SECONDARY ACCESSION(S): PRJNA95013

REPOSITORIES: GEO

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The Genome Wide Distribution of Acetylated Histone H4 Remodelled through Human Primary Myoblast Differentiation

Project description:The simultaneous genotyping of tens of thousands of SNP using SNP microarrays is a very important tool that is revolutionizing genetics and molecular biology. In this work, we present a new application of this technique by using it to assess chromatin immunoprecipitation (CHIP) as a means to assess the multiple genomic locations bound by a protein complex recognized by an antibody. We illustrate the use of this technique with an analysis of the change in histone H4 acetylation, a marker of open chromatin and transcriptionally active genomic regions, which occur during the differentiation of human myoblasts into myotubes. Our results are validated by the observation of a significant correlation between the histone modifications detected and the expression of the nearby genes, as measured by DNA microarrays. Keywords: SuperSeries This super series is composed of the following subset series: GSE4131: Triplicate Affymetrix HGU133A/B expression chips were hybridized to RNA extracted from myoblasts and myotubes. GSE4132: Triplicate Affymetrix 10K ax 13339 SNP chips were hybridized to DNA from myoblasts and myotubes.

2010-06-10 | E-GEOD-4133 | biostudies-arrayexpress

Mapping of H4-acetylated chromatin modifications in differentiating human primary myoblasts

Project description:We assessed the genomic distribution of H4-acetylated chromatin by ChIP using SNP chips and an antibody specific to four acetylated lysine residues of H4. Keywords: Comparative genomic hybridization

2006-08-28 | GSE4132 | GEO

ChIP-chip from Drosophila egg chambers using antibody recognizing tetra-acetylated histone H4

Project description:Chromatin immunoprecipitation of tetra-acetylated histone H4 followed by hybridization to genome-wide tiling microarrays demonstrated that tetra-acetylated H4 is enriched at the two chorion Drosophila amplicons in follicle cells (DAFC) as well as other non-amplified loci

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ChIP-chip from Drosophila egg chambers using antibody recognizing tetra-acetylated histone H4

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ENCODE ChIP-chip for Tetra-acetylated Histone H4 on GM06990 Cells [unpublished]

Project description:Tetra-acetylated Histone H4 ChIP-chip performed on GM06990 cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify acetylated Histone H4-binding regions. Use of this data requires permission from its producers. Keywords: ChIP-chip

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ENCODE ChIP-chip for Tetra-acetylated Histone H4 on HeLaS3 Cells [unpublished]

Project description:Tetra-acetylated Histone H4 ChIP-chip performed on HeLaS3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify Acetylated Histone H4-binding regions. Use of this data requires permission from its producers. Keywords: ChIP-chip

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Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain.

Project description:Recognition of acetylated chromatin by the bromodomains and extra-terminal domain (BET) family proteins is a hallmark for transcriptional activation and anchoring viral genomes to mitotic chromosomes of the host. One of the BET family proteins BRD2 interacts with acetylated chromatin during mitosis and leads to transcriptional activation in culture cells. Here, we report the crystal structures of the N-terminal bromodomain of human BRD2 (BRD2-BD1; residues 74-194) in complex with each of three different Lys-12-acetylated H4 peptides. The BRD2-BD1 recognizes the H4 tail acetylated at Lys-12 (H4K12ac), whereas the side chain of hypoacetylated Lys-8 of H4 binds at the cavity of the dimer interface of BRD2-BD1. From binding studies, we identified the BRD2-BD1 residues that are responsible for recognition of the Lys-12-acetylated H4 tail. In addition, mutation to Lys-8 in the Lys-12-acetylated H4 tail decreased the binding to BRD2-BD1, implicating the critical role of Lys-8 in the Lys-12-acetylated H4 tail for the recognition by BRD2-BD1. Our findings provide a structural basis for deciphering the histone code by the BET bromodomain through the binding with a long segment of the histone H4 tail, which presumably prevents erasure of the histone code during the cell cycle.

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Project description:ISWI is the catalytic subunit of several ATP-dependent chromatin remodelling factors that catalyse the sliding of nucleosomes along DNA and thereby endow chromatin with structural flexibility. Full activity of ISWI requires residues of a basic patch of amino acids in the N-terminal 'tail' of histone H4. Previous studies employing oligopeptides and mononucleosomes suggested that acetylation of the H4 tail at lysine 16 (H4K16) within the basic patch may inhibit the activity of ISWI. On the other hand, the acetylation of H4K16 is known to decompact chromatin fibres. Conceivably, decompaction may enhance the accessibility of nucleosomal DNA and the H4 tail for ISWI interactions. Such an effect can only be evaluated at the level of nucleosome arrays. We probed the influence of H4K16 acetylation on the ATPase and nucleosome sliding activity of Drosophila ISWI in the context of defined, in vitro reconstituted chromatin fibres with physiological nucleosome spacing and linker histone content. Contrary to widespread expectations, the acetylation did not inhibit ISWI activity, but rather stimulated ISWI remodelling under certain conditions. Therefore, the effect of H4K16 acetylation on ISWI remodelling depends on the precise nature of the substrate.

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Expression, purification and proteomic analysis of recombinant histone H4 acetylated at lysine 16.

Project description:Many histone covalent modifications have been identified and shown to play key regulatory roles in eukaryotic transcription, DNA damage repair, and replication. In vitro experiments designed to understand the mechanistic role of individual modifications require the availability of substantial quantities of pure histones, homogeneously modified at specific residues. We have applied the amber stop codon/suppressor tRNA strategy to the production of histone H4 acetylated at lysine 16, a particularly important isoform of this histone. Our success relies on adapting the H4 DNA sequence to the codon preference of E. coli and on preventing the premature decay of the H4 mRNA. These modifications to the original procedure render it easily applicable to the generation of any covalently modified histone H4 isoform.

| S-EPMC3771349 | biostudies-literature

Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies.

Project description:Antibodies specific for histone post-translational modifications (PTMs) have been central to our understanding of chromatin biology. Here, we describe an unexpected and novel property of histone H4 site-specific acetyl antibodies in that they prefer poly-acetylated histone substrates. By all current criteria, these antibodies have passed specificity standards. However, we find these site-specific histone antibodies preferentially recognize chromatin signatures containing two or more adjacent acetylated lysines. Significantly, we find that the poly-acetylated epitopes these antibodies prefer are evolutionarily conserved and are present at levels that compete for these antibodies over the intended individual acetylation sites. This alarming property of acetyl-specific antibodies has far-reaching implications for data interpretation and may present a challenge for the future study of acetylated histone and non-histone proteins.

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