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Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [RNA-seq]

ABSTRACT: Transcriptome in respect to H2A.Z downregulation or overexpression

ORGANISM(S): Fusarium fujikuroi

PROVIDER: GSE237762 | GEO | 2024/04/02

REPOSITORIES: GEO

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Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [ChIP-seq]

Project description:ChIP-seq of histone PTM and H2A.Z depositioning in F. fujikuroi

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Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi

Project description:This SuperSeries is composed of the SubSeries listed below.

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Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [Mnase-seq]

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2024-04-02 | GSE237764 | GEO

Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi

Project description:Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi

| PRJNA996564 | ENA

Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [RNA-seq]

Project description:Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [RNA-seq]

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Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [Mnase-seq]

Project description:Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [Mnase-seq]

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Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [ChIP-seq]

Project description:Novel insights into the role of the histone variant H2A.Z in the plant pathogen Fusarium fujikuroi [ChIP-seq]

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Incorporation of the histone variant H2A.Z counteracts gene silencing mediated by H3K27 trimethylation in Fusarium fujikuroi

Project description: Not available

| S-EPMC10953111 | biostudies-literature

Deposition of histone variant H2A.Z within gene bodies regulates responsive genes

Project description:The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that a loss of H2A.Z in Arabidopsis does not affect the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is caused by the exclusion of H2A.Z from methylated DNA. RNA-seq and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. We find that a loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to both endogenous and exogenous stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes. Examination of DNA methylation and transcription in an h2a.z mutant

2012-12-13 | E-GEOD-39045 | biostudies-arrayexpress

The histone variant H2A.Z is an important regulator of enhancer activity.

Project description:Gene regulatory programs in different cell types are largely defined through cell-specific enhancers activity. The histone variant H2A.Z has been shown to play important roles in transcription mainly by controlling proximal promoters, but its effect on enhancer functions remains unclear. Here, we demonstrate by genome-wide approaches that H2A.Z is present at a subset of active enhancers bound by the estrogen receptor alpha (ERα). We also determine that H2A.Z does not influence the local nucleosome positioning around ERα-enhancers using ChIP-sequencing at nucleosomal resolution and unsupervised pattern discovery. We further highlight that H2A.Z-enriched enhancers are associated with chromatin accessibility, H3K122ac enrichment and hypomethylated DNA. Moreover, upon estrogen stimulation, the enhancers occupied by H2A.Z produce enhancer RNAs (eRNAs), and recruit RNA polymerase II as well as RAD21, a member of the cohesin complex involved in chromatin interactions between enhancers and promoters. Importantly, their recruitment and eRNAs production are abolished by H2A.Z depletion, thereby revealing a novel functional link between H2A.Z occupancy and enhancer activity. Taken together, our findings suggest that H2A.Z acts as an important player for enhancer functions by establishing and maintaining a chromatin environment required for RNA polymerase II recruitment, eRNAs transcription and enhancer-promoters interactions, all essential attributes of enhancer activity. The MNase ChIP-seqs in this study measure the genome-wide binding landscape of H2A.Z, H3K4me1, H3K27ac and H3K4me3 in MCF-7 cells in the absence or presence of E2. Two biological replicates were done for each ChIP-seq experiment and for each condition, as well as, control input.

2015-08-31 | E-GEOD-57436 | biostudies-arrayexpress

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