Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing.

ABSTRACT: Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the s

SUBMITTER: Saha K 

PROVIDER: S-EPMC7293017 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature