Please use this identifier to cite or link to this item: https://doi.org/10.1261/rna.066951.118
Title: An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
Authors: Parra M.
Booth B.W.
Weiszmann R.
Yee B.
Yeo G.W. 
Brown J.B.
Celniker S.E.
Conboy J.G.
Keywords: Alternative splicing
Intron retention
SF3B1
Issue Date: 2018
Publisher: Cold Spring Harbor Laboratory Press
Citation: Parra M., Booth B.W., Weiszmann R., Yee B., Yeo G.W., Brown J.B., Celniker S.E., Conboy J.G. (2018). An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys. RNA 24 (9) : 699. ScholarBank@NUS Repository. https://doi.org/10.1261/rna.066951.118
Abstract: During terminal erythropoiesis, the splicing machinery in differentiating erythroblasts executes a robust intron retention (IR) program that impacts expression of hundreds of genes. We studied IR mechanisms in the SF3B1 splicing factor gene, which expresses ?50% of its transcripts in late erythroblasts as a nuclear isoform that retains intron 4. RNA-seq analysis of nonsense-mediated decay (NMD)-inhibited cells revealed previously undescribed splice junctions, rare or not detected in normal cells, that connect constitutive exons 4 and 5 to highly conserved cryptic cassette exons within the intron. Minigene splicing reporter assays showed that these cassettes promote IR. Genome-wide analysis of splice junction reads demonstrated that cryptic noncoding cassettes are much more common in large (>1 kb) retained introns than they are in small retained introns or in nonretained introns. Functional assays showed that heterologous cassettes can promote retention of intron 4 in the SF3B1 splicing reporter. Although many of these cryptic exons were spliced inefficiently, they exhibited substantial binding of U2AF1 and U2AF2 adjacent to their splice acceptor sites. We propose that these exons function as decoys that engage the intron-terminal splice sites, thereby blocking cross-intron interactions required for excision. Developmental regulation of decoy function underlies a major component of the erythroblast IR program. � 2018 Parra et al.
Source Title: RNA
URI: http://scholarbank.nus.edu.sg/handle/10635/152026
ISSN: 13558382
DOI: 10.1261/rna.066951.118
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