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Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [mRNA]

ABSTRACT: Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A.Bbd, a rapidly evolving variant found in mammals but not in invertebrates. We report that in human cells, nucleosomes bearing H2A.Bbd form unconventional chromatin structures enriched within actively transcribed genes and characterized by shorter DNA protection and nucleosome spacing. Analysis of transcriptional profiles from cells depleted for H2A.Bbd demonstrated widespread changes in gene expression with a net down-regulation of transcription and disruption of normal mRNA splicing patterns. In particular, we observed changes in exon inclusion rates and increased presence of intronic sequences in mRNA products upon H2A.Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE38890 | GEO | 2012/07/16

SECONDARY ACCESSION(S): PRJNA169141

REPOSITORIES: GEO

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Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [mRNA]

Project description:Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A.Bbd, a rapidly evolving variant found in mammals but not in invertebrates. We report that in human cells, nucleosomes bearing H2A.Bbd form unconventional chromatin structures enriched within actively transcribed genes and characterized by shorter DNA protection and nucleosome spacing. Analysis of transcriptional profiles from cells depleted for H2A.Bbd demonstrated widespread changes in gene expression with a net down-regulation of transcription and disruption of normal mRNA splicing patterns. In particular, we observed changes in exon inclusion rates and increased presence of intronic sequences in mRNA products upon H2A.Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing. Gene expression was measured in two replicates of the HeLa cells expressing H2A.Bbd-FLAG histone, which were treated with shRNA with no homology to the human genome.

2012-07-15 | E-GEOD-38890 | biostudies-arrayexpress

Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [ChIP-Seq]

Project description:Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A.Bbd, a rapidly evolving variant found in mammals but not in invertebrates. We report that in human cells, nucleosomes bearing H2A.Bbd form unconventional chromatin structures enriched within actively transcribed genes and characterized by shorter DNA protection and nucleosome spacing. Analysis of transcriptional profiles from cells depleted for H2A.Bbd demonstrated widespread changes in gene expression with a net down-regulation of transcription and disruption of normal mRNA splicing patterns. In particular, we observed changes in exon inclusion rates and increased presence of intronic sequences in mRNA products upon H2A.Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing. Nuclei were digested with Mnase and histone-DNA complexes were isolated with antibody.

2012-07-16 | E-GEOD-38284 | biostudies-arrayexpress

Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [ChIP-Seq]

2012-07-16 | GSE38284 | GEO

Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [RNA-Seq]

2012-07-16 | GSE38770 | GEO

Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells

Project description:Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A.Bbd, a rapidly evolving variant found in mammals but not in invertebrates. We report that in human cells, nucleosomes bearing H2A.Bbd form unconventional chromatin structures enriched within actively transcribed genes and characterized by shorter DNA protection and nucleosome spacing. Analysis of transcriptional profiles from cells depleted for H2A.Bbd demonstrated widespread changes in gene expression with a net down-regulation of transcription and disruption of normal mRNA splicing patterns. In particular, we observed changes in exon inclusion rates and increased presence of intronic sequences in mRNA products upon H2A.Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing. This SuperSeries is composed of the SubSeries listed below.

2012-07-16 | GSE38771 | GEO

Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells

Project description:Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A.Bbd, a rapidly evolving variant found in mammals but not in invertebrates. We report that in human cells, nucleosomes bearing H2A.Bbd form unconventional chromatin structures enriched within actively transcribed genes and characterized by shorter DNA protection and nucleosome spacing. Analysis of transcriptional profiles from cells depleted for H2A.Bbd demonstrated widespread changes in gene expression with a net down-regulation of transcription and disruption of normal mRNA splicing patterns. In particular, we observed changes in exon inclusion rates and increased presence of intronic sequences in mRNA products upon H2A.Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing. This SuperSeries is composed of the following subset Series: GSE38284: Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [ChIP-Seq] GSE38770: Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [RNA-Seq] GSE38890: Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [mRNA] Refer to individual Series

2012-07-15 | E-GEOD-38771 | biostudies-arrayexpress

Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [RNA-Seq]

Project description:Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A.Bbd, a rapidly evolving variant found in mammals but not in invertebrates. We report that in human cells, nucleosomes bearing H2A.Bbd form unconventional chromatin structures enriched within actively transcribed genes and characterized by shorter DNA protection and nucleosome spacing. Analysis of transcriptional profiles from cells depleted for H2A.Bbd demonstrated widespread changes in gene expression with a net down-regulation of transcription and disruption of normal mRNA splicing patterns. In particular, we observed changes in exon inclusion rates and increased presence of intronic sequences in mRNA products upon H2A.Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing. RNA-seq was used to examine changes in gene expression upon shRNA-assisted depletion of H2A.Bbd and H2A.Z histone variants in HeLa cells. The cells treated with shRNA with no homology to the human genome were used as control.

2012-07-16 | E-GEOD-38770 | biostudies-arrayexpress

H2A.Bbd localizes to DNA synthesis sites

Project description:Mass spectrometry analysis of chromatin-containing GFP-H2A.Bbd revealed an high enrichment of factors associated to replication compared to GFP-macroH2A.1.2 and GFP-H2A.

2014-05-18 | PXD000789 | Pride

Growth cone localization of the mRNA encoding a chromatin regulator modulates neurite outgrowth

Project description:Neurons exploit local mRNA translation and retrograde transport of transcription factors to regulate gene expression in response to signaling events at distal neuronal ends. Whether epigenetic factors could also be involved in such regulation is not known. We report that the mRNA encoding the HMGN5 chromatin binding protein localizes to growth cones of both neuronal-like cells and of hippocampal neurons, where it has the potential to be translated, and that HMGN5 can be retrogradely transported into the nucleus along neurites. Loss of HMGN5 function induces transcriptional changes and impairs neurite outgrowth while HMGN5 overexpression induces neurite outgrowth and chromatin decompaction. Interestingly, control of both neurite outgrowth and chromatin structure is dependent on growth cone localization of Hmgn5 mRNA. Our results provide the first evidence that mRNA localization and local translation might serve as a mechanism to couple the dynamic neuronal outgrowth process with chromatin regulation in the nucleus.

2015-04-17 | PXD001070 | Pride

Homo sapiens

Project description:Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [mRNA]

| PRJNA169141 | ENA