Novel features of miRNA and isomiR-mRNA interactions

Studying the interactions between microRNAs/isomiRs and mRNAs is critical due to their fundamental roles in gene regulation and their involvement in various diseases. Although many isomiRs have been identified, the analysis of their interactions with mRNAs remains in its early stages. In this study, we compiled available human chimeric read data, each comprising a microRNA or isomiR segment paired with an mRNA fragment and identified 1,747 isomiRs and over 5 million microRNA/isomiR–mRNA interactions. We observed that microRNAs with higher adenine and thymine content, and lower cytosine content, tend to have more isomiRs and more mRNA targets. Notably, an average of 18.9% of mRNA targets were bound exclusively by isomiRs, not by their microRNA counterparts. Furthermore, isomiRs sharing the same seed sequences as their reference microRNAs may bind to different targets from their microRNAs, highlighting functional divergence. Interestingly, 20.0% of microRNAs and 8.2% of isomiRs appear to bind mRNAs independently of their seed regions. Among those that do utilize seed regions, 94.5% of microRNAs and 95.7% of isomiRs also engage non-seed regions, suggesting a broader and more complex binding behavior. Our findings offer new insights into microRNA/isomiR–mRNA interactions.