Introns encode a vast class of Kink-loop RNAs that autoregulate pre-mRNA splicing
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. One Sentence Summary A huge class of orphan backward K-loop RNAs