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An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.

Marilyn Parra, Ben W Booth, Richard Weiszmann, Brian Yee, Gene W Yeo, James B Brown, Susan E Celniker, John G Conboy

RNA (New York, N.Y.) · 2018 · Vol. 24 (9) · pp. 1255-1265

PubMed ↗ DOI ↗ PMC full text ↗

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 <i>SF3B1</i> 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 <i>SF3B1</i> 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.

Potentially related datasets 2

These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.

Accession Source Title
ENCSR862QCH ENCSR · ENCODE eCLIP experiment on K562 against U2AF1
ENCSR893RAV ENCSR · ENCODE eCLIP experiment on K562 against U2AF2
Funding 6 grants
Grant Funder
R01 HG004659 NHGRI NIH HHS (United States)
U54 HG007005 NHGRI NIH HHS (United States)
R01 DK108020 NIDDK NIH HHS (United States)
R00 HG006698 NHGRI NIH HHS (United States)
R01 DK094699 NIDDK NIH HHS (United States)
S10 OD018174 NIH HHS (United States)