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

Research output: Contribution to journalArticlepeer-review


  • Marilyn Parra
  • Ben W Booth
  • Richard Weiszmann
  • Brian A Yee
  • Gene W Yeo
  • Susan E Celniker
  • John G Conboy

Colleges, School and Institutes

External organisations

  • Lawrence Berkeley National Laboratory
  • University of California, San Diego
  • Lawrence Berkeley National Laboratory;


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 (>1kb) retained introns than they are in small retained introns or in non-retained 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, blocking cross-intron interactions required for excision. Developmental regulation of decoy function underlies a major component of the erythroblast IR program.


Original languageEnglish
Pages (from-to)1255-1265
Number of pages11
Early online date29 Jun 2018
Publication statusE-pub ahead of print - 29 Jun 2018


  • SF3B1, alternative splicing, intron retention