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. 2024 Aug 20:920:148521.
doi: 10.1016/j.gene.2024.148521. Epub 2024 May 3.

Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress

Amanda Piveta Schnepper  1 , Lucas Farinazzo Marques  2 , Ivan Rodrigo Wolf  1 , Agatha M S Kubo  3 , Guilherme Targino Valente  4
Affiliations

Potential global cis and trans regulation of lncRNAs in Saccharomyces cerevisiae subjected to ethanol stress

Amanda Piveta Schnepper et al. Gene. .

Abstract

Long noncoding RNAs (lncRNAs) are regulatory RNAs. Saccharomyces cerevisiae strains transcribe hundreds of lncRNAs. LncRNAs can regulate the expression of adjacent genes (cis-regulation) or distant genes from lncRNAs (trans-regulation). Here, we analyzed the potential global cis and trans-regulation of lncRNAs of yeast subjected to ethanol stress. For potential cis regulation, for BMA641-A and S288C strains, we observed that most lncRNA-neighbor gene pairs increased the expression at a certain point followed by a decrease, and vice versa. Based on the transcriptome profile and triple helix prediction between lncRNAs and promoters of coding genes, we observed nine different ways of potential trans regulation that work in a strain-specific manner. Our data provide an initial landscape of potential cis and trans regulation in yeast, which seems to be strain-specific.

Keywords: Cis and trans regulation; Strain-specificity; lncRNAs.

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Conflict of interest statement

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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