Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes

Gene expression and regulation with or without alternative splicing are key factors for cells to properly function. Distant splicing quantitative trait loci (distant sQTLs) are genomic mutations that impact the alternative splicing patterns of far-away genes. Nevertheless, the procedures causing a distant sQTL to regulate the alternative splicing of genes are not well defined. Higher resolution chromosome conformation capture experiments like Micro-C or Hi-C together with an expanding number of sQTL datasets on humans help us in understanding the spatial processes governing distant sQTL relationships at a genome-wide scale. In this study, we focus on analyzing whether spatial closeness helps in regulating sQTL-gene interactions over high-order chromatin topological domain structure, which is inferred from chromosome conformation experiments. We discover larger-scale chromatin shape to be in line with sQTL associations. In detail, sQTLs are generally spatially near their splicing genes in 3D, they frequently appear near topologically associating domain (TAD) and frequently interacting region (FIRE) boundaries, and are favorably related to genes over TADs and FIREs. Additionally, we discover that inside-domain sQTLs accompanied by functional regulatory elements, including enhancers and promoters, are spatially closer than all inside-domain sQTLs. This result suggests that spatial closeness between sQTLs and their distant splicing genes obtained from chromatin's TAD structure has major importance in regulating alternative splicing and thus in gene regulation. Our results are robust across different experiments such as Hi-C and Micro-C, different TAD inference methods, different Hi-C binning resolutions, different alternative splicing events, and once we control for eQTLs, which are shown to be spatially close to their genes.