Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network.

Laura Natalia Balarezo-Cisneros,Catherine B Millar,Ping Wang,Steven Parker,Raymond T O’Keefe,Daniela Delneri,Soukaina Timouma,Marcin G Fraczek,Jonathan Houseley

doi:10.1371/journal.pgen.1008761

Laura Natalia Balarezo-Cisneros, Catherine B Millar + Show 7 more

Open Access

https://doi.org/10.1371/journal.pgen.1008761

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Journal: PLoS genetics	Publication Date: Jan 25, 2021
Citations: 19	License type: CC BY 4.0

Affiliation: University of Manchester

Abstract

Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response to different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT053, SUT468) or rRNA processing (SUT075 and snR30). Overall, these data capture and integrate the regulatory and phenotypic network of ncRNAs and protein-coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis.

Highlights

Gene regulation is a key biological process across all life forms, and multiple gene interactions quickly allow adaptation to different conditions in response to environmental stimuli
As the most significant fitness phenotypes observed for non-coding RNA (ncRNA) deletion mutant strains were in YP or YPD media supplemented with ethanol, we identified those transcription factors (TFs) whose mis-regulation has been linked to ethanol resistance
These results suggest that the global effect on the transcriptome observed in the absence of SUT126 is likely driven by an effect of this ncRNA on TFs such as Pdr3

Summary

Introduction

Gene regulation is a key biological process across all life forms, and multiple gene interactions quickly allow adaptation to different conditions in response to environmental stimuli. Saccharomyces cerevisiae (S. cerevisiae) lacks RNAi machinery; a large number of non-coding transcripts have been identified in this budding yeast using high-throughput and high-resolution technologies. These ncRNA transcripts come from what is known as “pervasive transcription”, a phenomenon that generates RNAs distinct from those that encode proteins or those with established functions (e.g. snoRNAs, snRNAs, rRNAs) [13]. Among a list of characterised pervasive transcripts, Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs) show an essential role in gene regulation, influencing histone modifications or regulating transcription of nearby genes [4, 5, 14,15,16]

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