Single-allele nanoscale mapping of regulatory variants

Millions of genetic variants are linked to human disease but identifying underlying mechanisms is challenging because most variants are noncausal and lie within the noncoding genome. We developed a Micro Capture-C variant-to-function platform (MCCv) based on analysis of single-allele chromatin structure. This can identify changes in nanoscale chromatin architecture and link variants in cis-regulatory elements to target genes. Furthermore, MCCv can phase other heterozygous variants within a locus to link regulatory variants to allelically imbalanced gene expression and directly read out variant effects on chromatin interactions after genome editing. With this approach, we investigated 405 cis-regulatory elements linked to immune-mediated inflammatory disease in CD4⁺ T cells. We uncovered a previously undescribed gain-of-function mechanism, which increases risk of autoimmunity through creation of a neo-CTCF motif that blocks super-enhancer contacts with the SESN3 promoter. We showed that SESN3 regulates mammalian target of rapamycin by sensing tryptophan and demonstrated its role in autoimmunity using mouse models.