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RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [Hi-C]

ABSTRACT: RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [Hi-C]

PROVIDER: PRJNA849655 | ENA |

REPOSITORIES: ENA

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RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [Hi-C]

Project description:Chicken erythrocytes are nucleated cells often referred to as transcriptionally inactive, although the epigenetic changes and chromatin remodeling that mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here we characterized the changes in gene expression, chromatin accessibility, genome organization, and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and found a complex chromatin reorganization at different genomic scales. We identified a robust decrease in transcription in erythrocytes. Nevertheless, a set of genes maintains their expression in erythrocytes, including genes involved in RNA pol II promoter-proximal pausing. Erythrocytes exhibit an inverted nuclear architecture and reposition euchromatin towards the nuclear periphery together with the paused RNA polymerase. In erythrocytes, chromatin domains are partially lost genome-wide except at mini domains retained around paused promoters. Our results suggest that promoter-proximal pausing of the RNA pol II participates in the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization.

2023-06-08 | GSE206192 | GEO

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

Project description:RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

| PRJNA849582 | ENA

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ATAC-seq]

2023-06-08 | GSE206191 | GEO

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ChIP-Seq]

2023-06-08 | GSE228694 | GEO

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [RNA-seq]

2023-06-08 | GSE206193 | GEO

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ChIP-Seq]

Project description:RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ChIP-Seq]

| PRJNA951220 | ENA

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ATAC-seq]

Project description:RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ATAC-seq]

| PRJNA849585 | ENA

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [RNA-seq]

Project description:RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [RNA-seq]

| PRJNA849587 | ENA

RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

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

2023-06-08 | GSE206194 | GEO

Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation: ChIP-chip data

Project description:Metazoan transcription is controlled through either coordinated recruitment of transcription machinery to the gene promoter, or subsequently, through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a key difference between genes that use these distinct regulatory strategies lies in the chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor nucleosomal occlusion of the promoter. Pausing of polymerase maintains these genes in an active state by inhibiting the formation of repressive promoter chromatin. In contrast, promoters of housekeeping genes that lack paused Pol II are deprived of nucleosomes regardless of polymerase binding, but show higher nucleosome occupancy downstream. Our results suggest that the âdefaultâ chromatin state of a gene instructs its regulation, and that highly-regulated promoters have evolved to encourage competition between nucleosomes and paused Pol II for promoter occupancy. All experiments were done using two channels per chip, comparing DNA immunoprecipitated by the indicated antibody to matching input chromatin used for affinity purification. Where appropriate, replicate data sets were averaged.

2010-10-18 | E-GEOD-20471 | biostudies-arrayexpress

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