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RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Gallus gallus

PROVIDER: GSE206194 | GEO | 2023/06/08

REPOSITORIES: GEO

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

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 | GSE206193 | GEO

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

2023-06-08 | GSE206192 | GEO

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

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 [Hi-C]

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

| PRJNA849655 | 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 [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 [ChIP-Seq]

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

| PRJNA951220 | ENA

Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis.

Project description:Piwi-interacting RNAs (piRNAs) are important for genome regulation across metazoans, but their biogenesis evolves rapidly. In Caenorhabditis elegans, piRNA loci are clustered within two 3-Mb regions on chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce an ∼28 nt primary transcript. We used comparative epigenomics across nematodes to gain insight into the origin, evolution, and mechanism of nematode piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA transcription. We describe two alternative modes of piRNA organization in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, while in other species, typified by Pristionchus pacificus, piRNAs are found within introns of active genes. Additionally, we discover that piRNA production depends on sequence signals associated with RNA polymerase II pausing. We show that pausing signals synergize with chromatin to control piRNA transcription.

| S-EPMC6436959 | biostudies-literature

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