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Genetic determinants of co-accessible chromatin regions in activated T cells across humans

ABSTRACT: Genetic determinants of co-accessible chromatin regions in activated T cells across humans

PROVIDER: PRJNA476685 | ENA |

REPOSITORIES: ENA

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Genetic determinants of co-accessible chromatin regions in activated T cells across humans

Project description:Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed Assay for Transposase-Accessible Chromatin (ATAC-seq) and RNA-seq profiles from activated primary CD4 + T cells of up to 105 healthy donors. We found that regions of chromatin accessibility (ATAC-peaks) are co-accessible at kilobase and megabase scales, in patterns consistent with the 3D organization of chromosomes measured by in situ Hi-C in T cells. Genetic variants located within ATAC-peaks often affected the accessibility of the corresponding peak and any co-accessible peaks. They also disrupt binding sites for transcription factors important for CD4 + T cell differentiation and activation, overlap and mediate expression QTLs from the same cells, and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression in primary immune cells that play a key role in many human diseases.

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Genetic determinants of co-accessible chromatin regions in activated T cells across humans.

Project description:Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression.

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