Circular RNA-associated QTLs show stronger association with splicing-QTLs than with expression-QTLs

Abstract

IntroductionCircular RNA quantitative trait locus (circQTLs) have emerged as a class of regulatory variants, but their mechanistic basis remains poorly characterized. Understanding how genetic variation influences circRNA biogenesis is essential to clarify their role in post-transcriptional gene regulation. MethodsWe systematically compared circQTLs with matched splicing (sQTL) and expression (eQTL) datasets. Using bootstrap-based Jaccard similarity analyses, we quantified genomic overlap patterns and assessed their statistical significance. We further validated these findings across independent circQTL studies. In addition, we analyzed the genomic distribution of circQTLs to identify enrichment patterns across functional genomic regions. ResultscircQTLs exhibited a statistically significant but modestly stronger genomic overlap with sQTLs compared to eQTLs. This pattern was consistent across independent datasets despite limited reproducibility of individual circQTL signals. Genomic annotation revealed distinct distributional patterns, including depletion in exonic regions and relative enrichment in non-coding genomic contexts compared to other QTL classes. DiscussionTogether, these results suggest that circRNA-associated regulatory variation is preferentially linked to splicing-related mechanisms rather than transcriptional control of host genes. However, the modest effect size indicates that this relationship is not exclusive, and likely reflects a mixture of shared splice-site regulatory effects and additional mechanisms specific to back-splicing that are not captured by conventional sQTL or eQTL frameworks. This dual architecture positions circRNA biogenesis at the interface between splicing dynamics, RNA structure, and higher-order genomic organization, supporting circQTLs as a distinct layer of post-transcriptional gene regulation.