The RNA binding protein Quaking represses splicing of the Fibronectin EDA exon and downregulates the interferon response

Abstract

Quaking (QKI) controls RNA metabolism in many biological processes including innate immunity, where its roles remain incompletely understood. To illuminate these roles, we performed genome scale transcriptome profiling in QKI knockout cells with or without poly(I:C) transfection, a double-stranded RNA analog that mimics viral infection. Analysis of RNA-sequencing data shows that QKI knockout upregulates genes induced by interferons, suggesting that QKI is an immune suppressor. Furthermore, differential splicing analysis shows that QKI primarily controls cassette exons, and among these events, we noted that QKI silences splicing of the extra domain A (EDA) exon in fibronectin (FN1) transcripts. QKI knockout results in elevated production and secretion of FN1-EDA protein, which is a known activator of interferons. Consistent with an upregulation of the interferon response in QKI knockout cells, our results show reduced production of dengue virus-2 and Japanese encephalitis virus in these cells. In conclusion, we demonstrate that QKI downregulates the interferon system and attenuates the antiviral state.

Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate

“…To explore the potential molecular mechanisms through which QKI regulates BIN1 exon 7 splicing, we generated a splicing reporter containing this exon, along with 126 bp of upstream and 184 bp of downstream intron sequence ( 41 ). Transfection of this reporter into HuH7 WT or QKI -KO cells ( 39 , 86 ) and analysis by RT-PCR showed a modest increase in exon 7 inclusion in the absence of QKI (Figure 6A ), consistent with QKI promoting skipping of this exon. Strikingly, the largest magnitude changes observed were an increase in unspliced reporter RNA and a decrease in exon 7 skipping (Figure 6A ).…”

Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate

“…To explore the potential molecular mechanisms through which QKI regulates BIN1 exon 7 splicing, we generated a splicing reporter containing this exon, along with 126 bp of upstream and 184 bp of downstream intron sequence (41). Transfection of this reporter into HuH7 WT or QKI-KO cells (39,86) and analysis by RT-PCR showed a modest increase in exon 7 inclusion in the absence of QKI (Fig 6A ), consistent with QKI promoting skipping of this exon. Strikingly, the largest magnitude changes observed were an increase in unspliced reporter RNA and a decrease in exon 7 skipping (Fig 6A).…”

An Unusual U2AF2 Inhibits Splicing and Attenuates the Virulence of the Human Protozoan Parasite Entamoeba histolytica

“…We observed that deletion of the KH-QUA2 domain increased the splicing efficiency of virulence-related transcripts indicating a splicing inhibitory function of such domain (Figure 1 and Table 1). This function was unforeseen; however, recently it has been described that QK1 (Quaking 1) inhibits the splicing cassette exons (Liao et al, 2021). QK1 is a member of the STAR domain-containing proteins, a domain composed of QUA1, KH, and QUA2 motifs that enable them to bind RNA recognition elements in vivo (Teplova et al, 2013) and to dimerize through their KH motif (Feracci et al, 2016).…”