Diverse environmental stresses elicit distinct responses at the level of pre-mRNA processing in yeast

Abstract

Gene expression in eukaryotic cells is profoundly influenced by the post-transcriptional processing of mRNAs, including the splicing of introns in the nucleus and both nuclear and cytoplasmic degradation pathways. These processes have the potential to affect both the steady-state levels and the kinetics of changes to levels of intron-containing transcripts. Here we report the use of a splicing isoform-specific microarray platform to investigate the effects of diverse stress conditions on pre-mRNA processing. Interestingly, we find that diverse stresses cause distinct patterns of changes at this level. The responses we observed are most dramatic for the RPGs and can be categorized into three major classes. The first is characterized by accumulation of RPG premRNA and is seen in multiple types of amino acid starvation regimes; the magnitude of splicing inhibition correlates with the severity of the stress. The second class is characterized by a rapid decrease in both pre-and mature RPG mRNA and is seen in many stresses that inactivate the TORC1 kinase complex. These decreases depend on nuclear turnover of the intron-containing pre-RNAs. The third class is characterized by a decrease in RPG pre-mRNA, with only a modest reduction in the mature species; this response is observed in hyperosmotic and cation-toxic stresses. We show that casein kinase 2 (CK2) makes important contributions to the changes in pre-mRNA processing, particularly for the first two classes of stress responses. In total, our data suggest that complex post-transcriptional programs cooperate to fine-tune expression of intron-containing transcripts in budding yeast.

RNA secondary structure mediates alternative 3′ss selection in Saccharomyces cerevisiae

“…Additionally, some of our predictions were previously reported as alternative 39ss (Davis et al 2000;Yassour et al 2009;Gahura et al 2011), which adds support to our proposed model, where premRNA secondary structure aids 39ss selection. Nonetheless, most of the splicing variation reported so far in yeast (Davis et al 2000;Preker et al 2002;Juneau et al 2007Juneau et al , 2009Pleiss et al 2007;Yassour et al 2009;Bergkessel et al 2011;Hossain et al 2011) corresponds to intron retention events and not to alternative 39ss selection and, hence, could not be recapitulated using our model. Using various yeast strains and conditions, we are able to experimentally validate a number of candidate alternative 39ss, further supporting our predictive model and confirming the existence of alternative 39ss selection in yeast.…”

“…S3). To the best of our knowledge, these two cases of alternative splicing have not been reported before in previous analyses of splicing variation in yeast (Davis et al 2000;Preker et al 2002;Juneau et al 2007Juneau et al , 2009Pleiss et al 2007;Yassour et al 2009;Bergkessel et al 2011;Hossain et al 2011). Some of the negative cases were shown before to have splicing variation different from alternative 39ss selection: HMF1 and REC102 Each predicted AG is given as the intron coordinates (chromosome, start, end, strand), the gene name, and the distance to the BS (calculated as explained in Materials and Methods).…”

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

“…Some previous studies have investigated the efficiency of splicing either for a specific intron or systematically for all introns, and under a variety of environmental conditions or in varying genetic backgrounds (Pleiss et al 2007;Bergkessel et al 2011;Pérez-Valle and Vilardell 2012). Such studies have demonstrated that different introns exhibit a large range of SEs under varying conditions and have diverse proteinaceous requirements (Clark et al 2002).…”

Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

“…RP genes produce the largest and most abundant class of spliced transcripts in yeast (Ares et al 1999;Cherry et al 2012), and RP gene expression and splicing are coherently regulated in response to a variety of environmental signals (Pleiss et al 2007;Bergkessel et al 2011). The majority of RP introns are required for growth in at least one condition (Parenteau et al 2011), supporting a regulatory role.…”