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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

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 erythrobla...

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Autores principales: Parra, Marilyn, Booth, Ben W., Weiszmann, Richard, Yee, Brian, Yeo, Gene W., Brown, James B., Celniker, Susan E., Conboy, John G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097662/
https://www.ncbi.nlm.nih.gov/pubmed/29959282
http://dx.doi.org/10.1261/rna.066951.118
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author Parra, Marilyn
Booth, Ben W.
Weiszmann, Richard
Yee, Brian
Yeo, Gene W.
Brown, James B.
Celniker, Susan E.
Conboy, John G.
author_facet Parra, Marilyn
Booth, Ben W.
Weiszmann, Richard
Yee, Brian
Yeo, Gene W.
Brown, James B.
Celniker, Susan E.
Conboy, John G.
author_sort Parra, Marilyn
collection PubMed
description 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.
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spelling pubmed-60976622019-09-01 An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys Parra, Marilyn Booth, Ben W. Weiszmann, Richard Yee, Brian Yeo, Gene W. Brown, James B. Celniker, Susan E. Conboy, John G. RNA Article 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. Cold Spring Harbor Laboratory Press 2018-09 /pmc/articles/PMC6097662/ /pubmed/29959282 http://dx.doi.org/10.1261/rna.066951.118 Text en © 2018 Parra et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Article
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
title An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
title_full An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
title_fullStr An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
title_full_unstemmed An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
title_short An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
title_sort important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097662/
https://www.ncbi.nlm.nih.gov/pubmed/29959282
http://dx.doi.org/10.1261/rna.066951.118
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