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

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 erythroblastmore » IR program.« less

Authors:
 [1];  [1];  [1];  [2];  [3];  [1];  [1];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of California, Berkeley, CA (United States)
  3. Univ. of California, Berkeley, CA (United States); National Univ. of Singapore (Singapore)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1480813
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Accepted Manuscript
Journal Name:
RNA
Additional Journal Information:
[ Journal Volume: 24; Journal Issue: 9]; Journal ID: ISSN 1355-8382
Publisher:
Cambridge University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Parra, Marilyn, Booth, Ben W., Weiszmann, Richard, Yee, Brian, Yeo, Gene W., Brown, James B., Celniker, Susan E., and Conboy, John G. An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys. United States: N. p., 2018. Web. doi:10.1261/rna.066951.118.
Parra, Marilyn, Booth, Ben W., Weiszmann, Richard, Yee, Brian, Yeo, Gene W., Brown, James B., Celniker, Susan E., & Conboy, John G. An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys. United States. doi:10.1261/rna.066951.118.
Parra, Marilyn, Booth, Ben W., Weiszmann, Richard, Yee, Brian, Yeo, Gene W., Brown, James B., Celniker, Susan E., and Conboy, John G. Fri . "An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys". United States. doi:10.1261/rna.066951.118. https://www.osti.gov/servlets/purl/1480813.
@article{osti_1480813,
title = {An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys},
author = {Parra, Marilyn and Booth, Ben W. and Weiszmann, Richard and Yee, Brian and Yeo, Gene W. and Brown, James B. and Celniker, Susan E. and Conboy, John G.},
abstractNote = {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.},
doi = {10.1261/rna.066951.118},
journal = {RNA},
number = [9],
volume = [24],
place = {United States},
year = {2018},
month = {6}
}

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    Works referencing / citing this record:

    Post‐Transcriptional Noise Control
    journal, June 2019