A termination-independent role of Rat1 in cotranscriptional splicing

Abstract

Rat1 is a 5′→3′ exoribonuclease in budding yeast. It is a highly conserved protein with homologs being present in fission yeast, flies, worms, mice and humans. Rat1 and its human homolog Xrn2 have been implicated in multiple nuclear processes. Here we report a novel role of Rat1 in mRNA splicing. We observed an increase in the level of unspliced transcripts in mutants of Rat1. Accumulation of unspliced transcripts was not due to the surveillance role of Rat1 in degrading unspliced mRNA, or an indirect effect of Rat1 function in termination of transcription or on the level of splicing factors in the cell, or due to an increased elongation rate in Rat1 mutants. ChIP-Seq analysis revealed Rat1 crosslinking to the introns of a subset of yeast genes. Mass spectrometry and coimmunoprecipitation revealed an interaction of Rat1 with the Clf1, Isy1, Yju2, Prp43 and Sub2 splicing factors. Furthermore, recruitment of splicing factors on the intron was compromised in the Rat1 mutant. Based on these findings we propose that Rat1 has a novel role in splicing of mRNA in budding yeast. Rat1, however, is not a general splicing factor as it crosslinks to only long introns with an average length of 400 nucleotides.

Yeast Dxo1 is required for 25S rRNA maturation and acts as a transcriptome-wide distributive exonuclease

“…These ribonucleases often have multiple functions, although in many cases their in vivo functions have not been fully defined. For example, the 5′ exoribonuclease Rat1 and the 3′ exoribonuclease the RNA exosome are both required for rRNA maturation, but they also have many other substrates, including released mRNA introns and aberrant RNAs ( Wasmuth and Lima 2012 ; Januszyk and Lima 2014 ; Dhoondia et al 2021 ). Yeast has proven to be a powerful eukaryotic system to initially identify ribonuclease functions, most of which are conserved in other eukaryotes, including humans.…”

Arabidopsis mRNA decay landscape shaped by XRN 5′‐3′ exoribonucleases

“…Loss of functional Xrn1 causes abnormal accumulation of intron‐retaining mRNAs in yeast (Dhoondia et al., 2021; Harigaya & Parker, 2012). In Arabidopsis, we noticed that xrn3‐3 but not xrn4‐6 possessed a considerable number of 5′P ends mapping to the 5′ splice sites of many introns, such as multiple introns in CPD and LHY (Figure 4a).…”