Spliceosome-mediated decay (SMD) regulates expression of nonintronic genes in budding yeast

Monica Passoni,Lidia Vasiljeva,Sneha Shah,Ralph D Hector,Adam Volanakis,Cornelia Kilchert,Sander Granneman

doi:10.1101/gad.221960.113

Monica Passoni, Lidia Vasiljeva + Show 5 more

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https://doi.org/10.1101/gad.221960.113

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Abstract

We uncovered a novel role for the spliceosome in regulating mRNA expression levels that involves splicing coupled to RNA decay, which we refer to as spliceosome-mediated decay (SMD). Our transcriptome-wide studies identified numerous transcripts that are not known to have introns but are spliced by the spliceosome at canonical splice sites in Saccharomyces cerevisiae. Products of SMD are primarily degraded by the nuclear RNA surveillance machinery. We demonstrate that SMD can significantly down-regulate mRNA levels; splicing at canonical splice sites in the bromodomain factor 2 (BDF2) transcript reduced transcript levels roughly threefold by generating unstable products that are rapidly degraded by the nuclear surveillance machinery. Regulation of BDF2 mRNA levels by SMD requires Bdf1, a functionally redundant Bdf2 paralog that plays a role in recruiting the spliceosome to the BDF2 mRNA. Interestingly, mutating BDF2 5' splice site and branch point consensus sequences partially suppresses the bdf1Δ temperature-sensitive phenotype, suggesting that maintaining proper levels of Bdf2 via SMD is biologically important. We propose that the spliceosome can also repress protein-coding gene expression by promoting nuclear turnover of spliced RNA products and provide an insight for coordinated regulation of Bdf1 and Bdf2 levels in the cell.

Highlights

The biogenesis of pre-mRNA involves multiple processing reactions, including 59 capping, splicing, cleavage, and polyadenylation at the 39 end, leading to production of translationally competent mRNA (Moore and Proudfoot 2009)
We demonstrate that splicing of these mRNAs at consensus splice sites generates unstable products that are primarily degraded by the nuclear RNA surveillance machinery
This spliceosome-mediated decay of bromodomain factor 2 (BDF2) mRNA is dependent on Bdf1, another bromodomain-containing protein, providing a plausible explanation of how expression of these paralogous genes is regulated

Summary

Introduction

The biogenesis of pre-mRNA involves multiple processing reactions, including 59 capping, splicing, cleavage, and polyadenylation at the 39 end, leading to production of translationally competent mRNA (Moore and Proudfoot 2009). The spliceosomal snRNPs and multiple non-snRNP proteins assemble cotranscriptionally on pre-mRNAs through recognition of the 59 splice site (59ss), the branch point (BP), and the 39ss to form the spliceosome (Carrillo Oesterreich et al 2011) This involves interactions of the spliceosomal components with the 59 cap-binding complex and the C-terminal domain (CTD) of RNA polymerase II (RNA Pol II). We demonstrate that splicing of these mRNAs at consensus splice sites generates unstable products that are primarily degraded by the nuclear RNA surveillance machinery This spliceosome-mediated decay (hereafter referred to as SMD) of BDF2 mRNA is dependent on Bdf, another bromodomain-containing protein, providing a plausible explanation of how expression of these paralogous genes is regulated. Our results have revealed a new role for the spliceosome in the regulation of mRNA expression

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