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

Amanda Piveta Schnepper; Lucas Farinazzo Marques; Ivan Rodrigo Wolf; Agatha M S Kubo; Guilherme Targino Valente

doi:10.1016/j.gene.2024.148521

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

Gene. 2024 May 3:920:148521. doi: 10.1016/j.gene.2024.148521. Online ahead of print.

Authors

Amanda Piveta Schnepper¹, Lucas Farinazzo Marques², Ivan Rodrigo Wolf¹, Agatha M S Kubo³, Guilherme Targino Valente⁴

Affiliations

¹ Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.
² Department of Bioprocess and Biotechnology, School of Agriculture, São Paulo State University (UNESP), Botucatu, SP, Brazil.
³ Laboratory of Applied Biotechnology, Sāo Paulo State University (UNESP), Botucatu, SP, Brazil.
⁴ Laboratory of Applied Biotechnology, Sāo Paulo State University (UNESP), Botucatu, SP, Brazil. Electronic address: valentegt@gmail.com.

PMID: 38703868
DOI: 10.1016/j.gene.2024.148521

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.