Abstract
The exosome is a complex with exoribonuclease activity that regulates RNA surveillance and turnover. The exosome also plays a role in regulating the degradation of precursor mRNAs to maintain the expression of splicing variants. In Neurospora, the silencing of rrp44, which encodes the catalytic subunit of the exosome, changed the expression of a set of spliceosomal snRNA, snRNP genes and SR protein related genes. The knockdown of rrp44 also affected the assembly of the spliceosome. RNA-seq analysis revealed a global change in bulk splicing events. Exosome-mediated splicing may regulate alternative splicing of NCU05290, NCU07421 and the circadian clock gene frequency (frq). The knockdown of rrp44 led to an increased ratio of splicing variants without intron 6 (I-6) and shorter protein isoform small FRQ (s-FRQ) as a consequence. These findings suggest that the exosome controls splicing events by regulating the degradation of precursor mRNAs and the gene expression, assembly and function of the spliceosome.
Highlights
The distribution of PRP5 protein in the sucrose density gradient fractions was evaluated by western blot analysis, and the results showed that the PRP5 levels increased in the fractionated samples from organisms grown in quinic acid (QA), suggesting that the knockdown of rrp[44] affects the levels of spliceosomal mRNA and the protein level of this spliceosomal component
The results showed that the knockdown of rrp[44] led to changes in at least four types of alternative splicing (AS) events: intron retention (IR), exon skipping (ES), alternative 5′ splice site selection (A5′ SS), and alternative 3′ splice site selection (A3′ SS)
The results showed that the ratio of small FRQ (s-FRQ)/large FRQ (l-FRQ) was increased in the dsrrp[44] strain in the presence of QA (Fig. 5G,H), which agrees with the RNA analysis
Summary
A growing body of evidence has suggested that alternative splicing plays a critical role in the regulation of circadian clocks in multiple species[13,14,15,16,17,18]. This work sheds light on the role of the exosome in the regulation of pre-mRNA splicing and the circadian clock
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