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

Parra, Marilyn; Zhang, Weiguo; Vu, Jonathan; DeWitt, Mark; Conboy, John G.

doi:10.1261/rna.075028.120

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

Journal Article · Mon Apr 20 00:00:00 EDT 2020 · RNA

DOI:https://doi.org/10.1261/rna.075028.120· OSTI ID:1756349

Parra, Marilyn ^[1]; Zhang, Weiguo ^[1]; Vu, Jonathan ^[2]; DeWitt, Mark ^[2]; Conboy, John G. ^[1]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of California, Berkeley, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231; 5R01DK108020

OSTI ID:: 1756349

Journal Information:: RNA, Vol. 26, Issue 8; ISSN 1355-8382

Publisher:: Cambridge University PressCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
SF3B1
alternative splicing
decoy exon
erythroid gene expression
intron retention

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

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