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Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE207954 | GEO | 2022/08/27

REPOSITORIES: GEO

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Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [Hi-C]

Project description:Although the 3D genome architecture is essential for long-range gene regulation, the significance of physical chromatin interactions is challenged by recent findings of mutual insensitiveness between contact propensity and gene expression. Here we report hundred basepair-resolution profiling of chromatin conformation in 33 colon tissues tracing the formation and malignant transformation of colorectal polyps. We identified progressive genome-wide decays of chromatin structures such as interaction stripes and loops on all types of cis-regulatory elements, particularly promoters, independent to the alterations of DNA methylation and chromatin accessibility. Instead of linearly correlated with degree of structural decays, transcription levels shifted toward correction of their quantitative mismatching with corresponding promoter contact propensity. These observations suggest increasing sensitivity of transcription to regulatory architecture integrity along with its loss during early cancer development, a mechanism which may provide novel insights to the misregulations of cancer driving genes.

2022-08-29 | GSE207951 | GEO

Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [ATAC-Seq]

2022-08-29 | GSE207950 | GEO

Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [RNA-Seq]

2022-08-29 | GSE207949 | GEO

Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [RNA-seq II]

2024-02-11 | GSE255300 | GEO

Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development

Project description:Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development

| PRJNA857730 | ENA

Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [RNA-Seq]

Project description:Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [RNA-Seq]

| PRJNA857731 | ENA

Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [Hi-C]

Project description:Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [Hi-C]

| PRJNA857732 | ENA

Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [ATAC-Seq]

Project description:Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [ATAC-Seq]

| PRJNA857733 | ENA

Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [RNA-seq II]

Project description:Global decay of regulatory chromatin architecture promotes rebalancing of gene expression during colorectal cancer development [RNA-seq II]

| PRJNA1074400 | ENA

Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution.

Project description:BackgroundBread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their interactions shape chromatin structure and gene expression in wheat. The open chromatin enrichment and network Hi-C (OCEAN-C) is a powerful antibody-independent method to detect chromatin interactions between open chromatin regions throughout the genome.ResultsHere we generate open chromatin interaction maps for hexaploid wheat and its tetraploid and diploid relatives using OCEAN-C. The anchors of chromatin loops show high chromatin accessibility and are concomitant with several active histone modifications, with 67% of them interacting with multiple loci. Binding motifs of various transcription factors are significantly enriched in the hubs of open chromatin interactions (HOCIs). The genes linked by HOCIs represent higher expression level and lower coefficient expression variance than the genes linked by other loops, which suggests HOCIs may coordinate co-expression of linked genes. Thousands of interchromosomal loops are identified, while limited interchromosomal loops (0.4%) are identified between homoeologous genes in hexaploid wheat. Moreover, we find structure variations contribute to chromatin interaction divergence of homoeologs and chromatin topology changes between different wheat species. The genes with discrepant chromatin interactions show expression alteration in hexaploid wheat compared with its tetraploid and diploid relatives.ConclusionsOur results reveal open chromatin interactions in different wheat species, which provide new insights into the role of open chromatin interactions in gene expression during the evolution of polyploid wheat.

| S-EPMC8785527 | biostudies-literature

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