We conclude that short introns are abundant in the human transcriptome, and short intron splicing represents an added layer to mRNA regulation.Ĭitation: Abebrese EL, Ali SH, Arnold ZR, Andrews VM, Armstrong K, Burns L, et al.
Our findings imply that standard gene prediction models which often assume a lower limit for intron size fail to predict short introns effectively. In many cases, splicing of these short introns from mRNAs is predicted to alter the reading frame and change protein output. Short intron splicing efficiency is increased by secondary structure, and we detect both canonical and non-canonical short introns. These short introns are often alternatively spliced and are found in a variety of RNAs–both mRNAs and lncRNAs. We identify hundreds of short introns conserved among multiple human cell lines. Here, we report an approach to identify RNA short introns from RNA-Seq data, discriminating against small genomic deletions. There have been some efforts to identify additional short introns, but little is known about how many short introns are processed from mRNAs. Non-canonical splicing–intron excision without the spliceosome–has been documented most notably, some tRNAs and the XBP1 mRNA contain short introns that are not removed by the spliceosome. Canonical pre-mRNA splicing requires snRNPs and associated splicing factors to excise conserved intronic sequences, with a minimum intron length required for efficient splicing.
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