The kink-turn (K-turn) is the most prevalent three-dimensional (3D) RNA structural motif in messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) 2, 3, 4. RNA structural motifs confer diversity of RNA architecture to regulate various biological processes 1. Taken together, our findings characterize a class of small RNAs and uncover another layer of gene expression regulation that involves crosstalk among bktRNAs, RNA splicing and RNA methylation. Most bktRNAs regulate the splicing of local introns by interacting with the 15.5K protein. Depletion of bktRNA1 causes global splicing dysregulation of U12-type introns by impairing the recruitment of ZCRB1 to the minor spliceosome. We found that a highly conserved bktRNA1 guides the methyltransferase fibrillarin to install RNA methylation of U12 small nuclear RNA in humans. All bktRNAs share two consensus sequence motifs at their fixed terminal position and have complex folding properties, expression and evolution patterns. In this study, we developed the RIP-PEN-seq method to identify the full-length sequences of RNAs bound by the K-turn binding protein 15.5K and discovered a previously uncharacterized class of RNAs with backward K-turn motifs (bktRNAs) in humans and mice. A kink-turn (K-turn) is a three-dimensional RNA structure that exists in all three primary phylogenetic domains.

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