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Title: Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts

Abstract

The decoy exon model has been proposed to regulate a subset of intron retention (IR) events involving predominantly larger introns (>1 kb). Splicing reporter studies have shown that decoy splice sites are essential for activity, suggesting that decoys act by engaging intron-terminal splice sites and competing with cross-intron interactions required for intron excision. The decoy model predicts that antisense oligonucleotides may be able to block decoy splice sites in endogenous pre-mRNA, thereby reducing IR and increasing productive gene expression. Indeed, we now demonstrate that targeting a decoy 5' splice site in the O-GlcNAc transferase (OGT) gene reduced IR from ~80% to ~20% in primary human erythroblasts, accompanied by increases in spliced OGT RNA and OGT protein expression. The remaining OGT IR was refractory to antisense treatment and might be mediated by independent mechanism(s). In contrast, other retained introns were strongly dependent on decoy function, since antisense targeting of decoy 5' splice sites greatly reduced (SNRNP70) or nearly eliminated (SF3B1) IR in two widely expressed splicing factors, and also greatly reduced IR in transcripts encoding the erythroid-specific structural protein, α-spectrin (SPTA1). These results show that modulating decoy exon function can dramatically alter IR and suggest that dynamic regulation of decoy exonsmore » could be a mechanism to fine-tune gene expression post-transcriptionally in many cell types.« less

Authors:
 [1];  [1];  [2];  [2];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
OSTI Identifier:
1756349
Grant/Contract Number:  
AC02-05CH11231; 5R01DK108020
Resource Type:
Accepted Manuscript
Journal Name:
RNA
Additional Journal Information:
Journal Volume: 26; Journal Issue: 8; Journal ID: ISSN 1355-8382
Publisher:
Cambridge University Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; SF3B1; alternative splicing; decoy exon; erythroid gene expression; intron retention

Citation Formats

Parra, Marilyn, Zhang, Weiguo, Vu, Jonathan, DeWitt, Mark, and Conboy, John G. Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts. United States: N. p., 2020. Web. doi:10.1261/rna.075028.120.
Parra, Marilyn, Zhang, Weiguo, Vu, Jonathan, DeWitt, Mark, & Conboy, John G. Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts. United States. https://doi.org/10.1261/rna.075028.120
Parra, Marilyn, Zhang, Weiguo, Vu, Jonathan, DeWitt, Mark, and Conboy, John G. Mon . "Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts". United States. https://doi.org/10.1261/rna.075028.120. https://www.osti.gov/servlets/purl/1756349.
@article{osti_1756349,
title = {Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts},
author = {Parra, Marilyn and Zhang, Weiguo and Vu, Jonathan and DeWitt, Mark and Conboy, John G.},
abstractNote = {The decoy exon model has been proposed to regulate a subset of intron retention (IR) events involving predominantly larger introns (>1 kb). Splicing reporter studies have shown that decoy splice sites are essential for activity, suggesting that decoys act by engaging intron-terminal splice sites and competing with cross-intron interactions required for intron excision. The decoy model predicts that antisense oligonucleotides may be able to block decoy splice sites in endogenous pre-mRNA, thereby reducing IR and increasing productive gene expression. Indeed, we now demonstrate that targeting a decoy 5' splice site in the O-GlcNAc transferase (OGT) gene reduced IR from ~80% to ~20% in primary human erythroblasts, accompanied by increases in spliced OGT RNA and OGT protein expression. The remaining OGT IR was refractory to antisense treatment and might be mediated by independent mechanism(s). In contrast, other retained introns were strongly dependent on decoy function, since antisense targeting of decoy 5' splice sites greatly reduced (SNRNP70) or nearly eliminated (SF3B1) IR in two widely expressed splicing factors, and also greatly reduced IR in transcripts encoding the erythroid-specific structural protein, α-spectrin (SPTA1). These results show that modulating decoy exon function can dramatically alter IR and suggest that dynamic regulation of decoy exons could be a mechanism to fine-tune gene expression post-transcriptionally in many cell types.},
doi = {10.1261/rna.075028.120},
journal = {RNA},
number = 8,
volume = 26,
place = {United States},
year = {Mon Apr 20 00:00:00 EDT 2020},
month = {Mon Apr 20 00:00:00 EDT 2020}
}

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