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

Authors: 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

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 exons could be a mechanism to fine-tune gene expression post-transcriptionally in many cell types.

Keywords

570, Erythroblasts, Cells, Bioinformatics and Computational Biology, Oligonucleotides, N-Acetylglucosaminyltransferases, intron retention, Article, decoy exon, alternative splicing, Genetics, RNA Precursors, Humans, Antisense, Cells, Cultured, Cultured, SF3B1, Exons, Biological Sciences, Oligonucleotides, Antisense, Introns, Alternative Splicing, Biochemistry and cell biology, erythroid gene expression, Biochemistry and Cell Biology, RNA Splice Sites, RNA Splicing Factors, Developmental Biology

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    influence
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
9
Top 10%
Average
Top 10%
Green
hybrid