Additional layer of regulation via convergent gene orientation in yeasts

Abstract

words)Convergent gene pairs can produce transcripts with complementary sequences. We had shown that mRNA duplexes form in vivo in Saccharomyces cerevisiae via interactions of mRNA overlapping 3'-ends and can lead to post-transcriptional regulatory events. Here we show that mRNA duplex formation is restricted to convergent genes separated by short intergenic distance, independently of their 3'-UTR length. We disclose an enrichment in genes involved in biological processes related to stress among these convergent genes. They are markedly conserved in convergent orientation in budding yeasts, meaning that this mode of post-transcriptional regulation could be shared in these organisms, conferring an additional level for modulating stress response. We thus investigated the mechanistic advantages potentially conferred by 3'-UTR mRNA interactions. Analysis of genome-wide transcriptome data revealed that Pat1 and Lsm1 factors, having 3'-UTR binding preference and participating to the remodeling of messenger ribonucleoprotein particles, bind differently these messenger interacting mRNAs (mimRNAs) forming duplexes in comparison to mRNAs that do not interact (solo mRNAs). Functionally, mimRNAs show limited translational repression upon stress. We thus propose that mRNA duplex formation modulates the regulation of mRNA expression by limiting their access to translational repressors. Our results thus show that posttranscriptional regulation is an additional factor that determines the order of coding genes.

Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq

“… 23 Convergent gene pairs can also form mRNA–mRNA interactions that regulate expression post-transcriptionally. 24 Nearly 90% of the 1500 IGRs in K. phaffii for which there were no recovered accessibility peaks were convergent with a median size less than 50 bp and might form such interactions. Disruption of these interactions by integration of a heterologous construct may disrupt cellular functions since gene pairs that form these interactions are often conserved and associated with stress response.…”

“…Disruption of these interactions by integration of a heterologous construct may disrupt cellular functions since gene pairs that form these interactions are often conserved and associated with stress response. 24 Codirectional genes may be coregulated by a single promoter, while expression of divergent genes may be driven by a bidirectional promoter. Additionally, the orientation of an IGR is correlated with its size, with convergent IGRs being significantly smaller than divergent or codirectional IGRs ( Figure 2 B).…”

Hybrid Sequencing Reveals Novel Features in the Transcriptomic Organization of Equid Alphaherpesvirus 1

“…This genomic organization suggests the existence of genome-wide transcriptional interference, caused by the collision and/or competition of the transcription apparatuses, which represent a novel level of genetic regulation (Boldogkői et al, 2012). The role of genomic context in the regulation of gene expression has recently been described in yeast (Gilet et al, 2020;Brooks et al, 2022).…”