BUD13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7

Abstract

Intron retention (IR) has emerged as an important mechanism of gene expression control, but the factors controlling IR events remain poorly understood. We observed consistent IR in one intron of the Irf7 gene and identified BUD13 as an RNA-binding protein that acts at this intron to increase the amount of successful splicing. Deficiency in BUD13 was associated with increased IR, decreased mature Irf7 transcript and protein levels, and consequently a dampened type I interferon response, which compromised the ability of BUD13-deficient macrophages to withstand vesicular stomatitis virus (VSV) infection. Global analysis of BUD13 knockdown and BUD13 cross-linking to RNA revealed a subset of introns that share many characteristics with the one found in Irf7 and are spliced in a BUD13-dependent manner. Deficiency of BUD13 led to decreased mature transcript from genes containing such introns. Thus, by acting as an antagonist to IR, BUD13 facilitates the expression of genes at which IR occurs. (A) Outline of the RAP-MS procedure used to identify RNA-binding proteins on transcripts of interest. (B) TMT ratio (Irf7/ActB) for proteins identified as enriched on either Irf7 (TMT ratio >1) or ActB (TMT ratio <1) transcripts. (C) qRT-PCR analysis of transcripts captured via RAP for Irf7 (blue) and ActB (gold) probes. (D) RIP followed by qRT-PCR for Irf7 and Rpl32 in TNF-a-stimulated BMDMs. Shown is the relative enrichment of transcripts captured in BUD13 RIP as compared to rabbit IgG RIP. (E) Same as (D), except stimulation with poly(I:C). Data are representative of two independent experiments (C-E) and presented as mean (error bars indicate SD). *p < 0.05, **p < 0.01 and ***p < 0.001, Student's t test.

Long non‐coding RNA DBH‐AS1 promotes cancer progression in diffuse large B‐cell lymphoma by targeting FN1 via RNA‐binding protein BUD13

“…In Figure 2D, antibodies against BUD13 precipitated a great amount of DBH-AS1. Besides, IRF7 was the positive control due to its binding relation with BUD13 mRNA (Frankiw et al, 2019), U6 served as negative control. In the meantime, a majority of BUD13 was pulled down by biotinylated DBH-AS1, and biotinylated DBH-AS1 AS group served as the negative control, Input as positive control (Figure 2E).…”

Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring

“…Alternatively, introns may be regulated by so many different proteins that no single binding motif is strongly predictive. Proteins including PTBP1 and others known to regulate particular retained introns demonstrate that such factors can be found (Yap et al, 2012;Horan et al, 2015;Frankiw et al, 2019b), but there may be many such factors each regulating a subset of introns in a group. The extension of our approach to larger datasets will allow correlation of changes in intron group assignment with the expression of particular RNA binding proteins.…”

Alternative mRNA Processing of Innate Response Pathways in Respiratory Syncytial Virus (RSV) Infection

“…One mechanistic study examining IRF7 processing described that inducible expression of alternatively spliced IRF7 transcripts with a GC-rich intron and a weak 5 splice site occurred. This study established alternative splicing decreased mature IRF7 transcripts and protein levels [60]. Here, expression of the intron-retained IRF7-isoform-dampened type I IFN response to single-stranded virus infection.…”