Introns encode a vast class of Kink-loop RNAs that autoregulate pre-mRNA splicing

Authors

Li, B., Lin, Q., Liu, A., Gan, H., Liu, S., Zheng, W., Liang, Y., Wan, G., Qu, L., Yang, J.

Abstract

Introns occupy nearly one-third of the human genome, yet whether they encode widespread regulatory functions remains unclear. Here, we identify a pervasive class of intron-derived Kink-loop RNAs (klRNAs) that locally control pre-mRNA processing. Using complementary enrichment strategies, we uncovered approximately 15,200 and 3,500 previously unannotated klRNAs in humans and mice, respectively. Bound by the conserved RNA-binding protein 15.5K, klRNAs constitute a distinct family of structured RNAs that arise predominantly from introns, lack the canonical stems of Kink-turn motifs, and do not exhibit antisense complementarity to known non-coding RNAs. Depletion of 15.5K disrupts klRNA biogenesis and leads to their global loss. Transcriptome-wide analyses reveal that klRNAs function predominantly in cis to suppress excision of their host introns in a kink-loop structure-dependent manner, thereby enabling introns to regulate their own processing. Together, our findings establish RNA structure-encoded autoregulation as a pervasive mechanism controlling intron fate and reveal that introns are active sources of regulatory RNAs.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 05 Aug 2026.

Stats

1-terrible, 9-excellent. How would you rate this preprint? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.