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Mechanistic insights into human pre-mRNA splicing of human ultra-short introns: potential unusual mechanism identifies G-rich introns

, : Mechanistic insights into human pre-mRNA splicing of human ultra-short introns: potential unusual mechanism identifies G-rich introns. Biochemical and Biophysical Research Communications 423(2): 289-294

It is unknown how very short introns (<65 nt; termed ultra-short introns) could be spliced in a massive spliceosome (>2.7 MDa) without steric hindrance. By screening an annotated human transcriptome database (H-InvDB), we identified three model ultra-short introns: the 56-nt intron in the HNRNPH1 gene, the 49-nt intron in the NDOR1 (NADPH dependent diflavin oxidoreductase 1) gene, and the 43-nt intron in the ESRP2 (epithelial splicing regulatory protein 2) gene. We verified that these endogenous ultra-short introns are spliced, and also recapitulated this in cultured cells transfected with the corresponding mini-genes. The splicing of these ultra-short introns was repressed by a splicing inhibitor, spliceostatin A, suggesting that SF3b (a U2 snRNP component) is involved in their splicing processes. The 56-nt intron containing a pyrimidine-rich tract was spliced out in a lariat form, and this splicing was inhibited by the disruption of U1, U2, or U4 snRNA. In contrast, the 49- and 43-nt introns were purine-rich overall without any pyrimidine-rich tract, and these lariat RNAs were not detectable. Remarkably, shared G-rich intronic sequences in the 49- and 43-nt introns were required for their splicing, suggesting that these ultra-short introns may recruit a novel auxiliary splicing mechanism linked to G-rich intronic splicing enhancers. We identified and characterized ultra-short introns (<65-nt) of human pre-mRNAs. The 56-, 49-, and 43-nt introns were found in the HNRNPH1, NDOR1, and ESRP2 genes. SF3b (U2 snRNP component) is involved in splicing of these 3 ultra-short introns. Splicing of the 56-nt intron requires the U1, U2, and U4 snRNPs. Splicing of the 49- and 43-nt introns requires G-rich intronic splicing enhancers.


PMID: 22640740

DOI: 10.1016/j.bbrc.2012.05.112

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