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Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [ChIP-seq]

ABSTRACT: Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [ChIP-seq]

PROVIDER: PRJNA529175 | ENA |

REPOSITORIES: ENA

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Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes

Project description:Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes

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Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [RNA-seq]

Project description:Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [RNA-seq]

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Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [ChIP-seq]

2020-12-31 | GSE128864 | GEO

Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes

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

2020-12-31 | GSE141015 | GEO

Atypical chromatin structure of immune-related genes expressed in chicken erythrocytes [RNA-seq]

Project description:Transcriptional regulation is impacted by multiple layers of genome organization. Here, we report that immune genes were associated with H3K4me3 and H3K27ac. In conjunction with next-generation DNA, RNA sequencing, chromatin immunoprecipitation-DNA sequencing and FAIRE sequencing, we identified the active chromosomal compartments and determined their structural signatures in relation to expression levels.

2020-12-31 | GSE141014 | GEO

Chicken erythrocytes stimulated with LPS, PGN and Poly(I:C)

2011-11-22 | GSE33813 | GEO

Chicken erythrocytes stimulated with LPS, PGN and Poly(I:C)

Project description:Erythrocytes represent the most abundant cell type of the bloodstream in all vertebrates. The principal feature that differenciates erythrocytes of non-mammals is that unlike mammals they mantain the nucleus in their terminal differentiation. While the main function associated to erythrocytes is the oxygen and carbon dioxide transport, some other functions, no less important, have been attributed to these cells. The focus of this study was to investigate the response of cultured chicken erythrocytes to bacterial lipopolysaccharide (LPS), bacterial peptidoglycan (PGN) and to the analog viral dsRNA Poly(I:C) using a comercial microarray platform from Agilent. Chicken erythrocytes were isolated from blood by twice Ficoll 1.007 density gradient centrifugations. For primary cell culture, erythrocytes were resuspended in DMEM (PAA Laboratories) supplemented with 10% heat-inactivated fetal bovine serum (FBS, PAA Laboratories) and the antibiotic Primocin (100 μg/ml, Invivogen) at a density of 7.5x106 cells/ml in six well cell culture plates (NUNC) and cultured at 37ºC and 5% CO2. Erythrocytes were stimulated with LPS from E. coli (serotype 0111:B4, Sigma) and Poly(I:C) (Invivogen) at 50 μg/ml, and with peptidoglycan from E.coli (0111:B4, Invivogen) at 5 μg/ml. All culture plates were incubated for 12h. Total RNA was extracted from the cultures using 1 ml of Tri Reagent (Sigma) following the manufacturer’s instructions with minor modifications. Quantity and integrity was analyzed by Nanodrop1000 (ThermoScientific) and Bioanalyzer 2100 (Agilent Technologies) respectively. Three biological replicates were used.

2011-11-22 | E-GEOD-33813 | biostudies-arrayexpress

3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin [Hi-C]

Project description:We present the first Hi-C map of non-mammalian vertebrate, Gallus gallus (domestic chicken). We show the presence of TADs in chicken embryonic fibroblast genome, distributed in accordance with gene density, transcriptional activity, and CTCF binding sites localization. In contrast to mammals, where all examined cell types display relatively similar chromatin architecture profile, in mature and immature chicken erythrocytes we identify unique chromatin spatial organization strongly differed from fibroblasts. Comparing mammalian and chicken genome architectures, we provide evidence highlighting evolutionary role of spatial organization and their significance in genome activity and regulation.

2017-03-10 | GSE96037 | GEO

Genomic location of H4R3me2a and H3R2me2s in chicken polychromatic erythrocytes

Project description:Genomic location of H4R3me2a and H3R2me2s in chicken polychromatic erythrocytes

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RNA polymerase II pausing contributes to maintain chromatin organization in erythrocytes [ChIP-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 | GSE228694 | GEO

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