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Identifying genetic variants associated with chromatin looping and genome function
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Identifying genetic variants associated with chromatin looping and genome function
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Journal Article
Identifying genetic variants associated with chromatin looping and genome function
2024
Overview
Here we present a comprehensive HiChIP dataset on naïve CD4 T cells (nCD4) from 30 donors and identify QTLs that associate with genotype-dependent and/or allele-specific variation of HiChIP contacts defining loops between active regulatory regions (iQTLs). We observe a substantial overlap between iQTLs and previously defined eQTLs and histone QTLs, and an enrichment for fine-mapped QTLs and GWAS variants. Furthermore, we describe a distinct subset of nCD4 iQTLs, for which the significant variation of chromatin contacts in nCD4 are translated into significant eQTL trends in CD4 T cell memory subsets. Finally, we define connectivity-QTLs as iQTLs that are significantly associated with concordant genotype-dependent changes in chromatin contacts over a broad genomic region (e.g., GWAS SNP in the
RNASET2
locus). Our results demonstrate the importance of chromatin contacts as a complementary modality for QTL mapping and their power in identifying previously uncharacterized QTLs linked to cell-specific gene expression and connectivity.
Here, the authors present an HiChIP dataset on naïve CD4 T cells from 30 donors. They investigate genotype-dependent and allele-specific variation of chromatin loops between active regulatory elements, reporting loop-associated variants linked to dynamic changes in gene expression.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
