Identifying genetic variants associated with chromatin looping and genome function

Sourya Bhattacharyya () and Ferhat Ay ()
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Sourya Bhattacharyya: La Jolla Institute for Immunology
Ferhat Ay: La Jolla Institute for Immunology

Nature Communications, 2024, vol. 15, issue 1, 1-22

Abstract: Abstract 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.

Date: 2024
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DOI: 10.1038/s41467-024-52296-4

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