ИСТИНА

RNA structure plays an essential role in the maturation of eukaryotic transcripts. While most current studies are focused on locally-occurring RNA structures, longrange base pairings have been increasingly reported as being implicated in the regulation of pre-mRNA splicing. This study aims at the validation of several targets from a recently published catalog of conserved long-range RNA structures. We studied the impact of long-range complementary interactions on splicing in three human genes — Phf20l1, Cask, and Ate. In Phf20l1 and Cask, in which alternative exons are located in between the complementary regions, we confirmed the looping-out mechanism of splicing regulation using compensatory mutations in minigenes. Additionally, we were able to change the alternative splicing outcome of the endogenous transcripts using steric blocking LNA-based antisense oligonucleotides. In Ate1, we demonstrated that two RNA structure modules coexist, one responsible for mutually exclusive exon choice (MXE) and the other regulating the ratio of transcript isoforms. We showed that Ate1 contains five conserved regulatory intronic elements R1–R5, of which R1 and R4 compete for base pairing with R3, while R2 and R5 form an ultra-long-range RNA structure spanning 30 Kb. In minigenes, single and double mutations that disrupt base pairings in R1R3 and R3R4 lead to the loss of MXE splicing, while compensatory triple mutations that restore RNA structure revert splicing to that of the wild type. In the endogenous Ate1 pre-mRNA, blocking the competing base pairings by LNA-based antisense oligonucleotides complementary to R3 leads to the loss of MXE splicing, while the disruption of R2R5 interaction changes the ratio of MXE. That is, Ate1 splicing is controlled by two independent, dynamically interacting, and functionally distinct RNA structure modules. The MXE ratio in Ate1 changes in response to RNA polymerase II slowdown, however it fails to do so when the ultra-long-range R2R5 interaction is disrupted, indicating that exon ratio depends on co-transcriptional RNA folding. To check whether a similar response also takes places in other genes, we performed an RNA-seq experiment using RNA polymerase II slowdown with 𝛼-amanitin. We found that introns with predicted long-range RNA structures respond to RNA polymerase II slowdown more than introns without such structures do, indicating that co-transcriptional RNA folding affects pre-mRNA splicing in a transcriptome-wide manner. In sum, our results demonstrate that splicing is coordinated both in time and in space over very long distances and that the interaction of these components is mediated by long-range RNA structure