The RNAPII-CTD Maintains Genome Integrity through Inhibition of Retrotransposon Gene Expression and Transposition

Abstract

RNA polymerase II (RNAPII) contains a unique C-terminal domain that is composed of heptapeptide repeats and which plays important regulatory roles during gene expression. RNAPII is responsible for the transcription of most protein-coding genes, a subset of non-coding genes, and retrotransposons. Retrotransposon transcription is the first step in their multiplication cycle, given that the RNA intermediate is required for the synthesis of cDNA, the material that is ultimately incorporated into a new genomic location. Retrotransposition can have grave consequences to genome integrity, as integration events can change the gene expression landscape or lead to alteration or loss of genetic information. Given that RNAPII transcribes retrotransposons, we sought to investigate if the RNAPII-CTD played a role in the regulation of retrotransposon gene expression. Importantly, we found that the RNAPII-CTD functioned to maintaining genome integrity through inhibition of retrotransposon gene expression, as reducing CTD length significantly increased expression and transposition rates of Ty1 elements. Mechanistically, the increased Ty1 mRNA levels in the rpb1-CTD11 mutant were partly due to Cdk8-dependent alterations to the RNAPII-CTD phosphorylation status. In addition, Cdk8 alone contributed to Ty1 gene expression regulation by altering the occupancy of the gene-specific transcription factor Ste12. Loss of STE12 and TEC1 suppressed growth phenotypes of the RNAPII-CTD truncation mutant. Collectively, our results implicate Ste12 and Tec1 as general and important contributors to the Cdk8, RNAPII-CTD regulatory circuitry as it relates to the maintenance of genome integrity.

Transcriptional coupling of telomeric retrotransposons with the cell cycle

“…Despite decades of research into the mechanisms of TRs in regulating telomere length in Drosophila , the specific transcription factors that control TR transcription remain unknown. In the budding yeast Saccharomyces cerevisiae , two transcriptional activators – Ste12 and Tec1 – are reported to regulate the expression of the Ty1 retrotransposons (Aristizabal et al, 2015). In addition, certain non-essential yeast Mediator subunits regulate the expression of Ty1 (Salinero et al, 2018).…”

Modulators of MAPK pathway activity during filamentous growth inSaccharomyces cerevisiae

“…Ste12p and Tec1p also regulate the cyclin-dependent kinase Cdk8p, controlling RNAPII-C-terminal domain to maintain genome integrity (N elson et al . 2003; A ristizabal et al . 2015).…”

A single flexible RNAPII-CTD integrates many different transcriptional programs

“… 5 Focusing on gene expression, shortening the CTD affects mRNA levels of a subset of genes, suggesting that like CTD sequence, CTD length contributes to gene expression in a loci-specific manner. 23-25 For instance, early work in S. cerevisiae unveiled a role for the CTD in activated transcription in particular conditions by showing reduced induction of the GAL10 and INO1 genes when the CTD was truncated, although induction of HIS4 was unaffected [ Fig. 2 denoted (YSPTSPS)x11].…”

“… 24 Most recently, the RNAPII-CTD was also shown to limit the expression of Ty1 retrotransposons, thus directly functioning in the maintenance of genome stability. 23 Although the molecular underpinnings of negative functions for the RNAPII-CTD remain to be fully determined, the increased expression levels of Rpn4-regulated genes and Ty1 retrotransposons were mediated by changes in promoter activity and suppressed by loss of the SRB10/CDK8 gene, which encodes the kinase subunit of the Mediator complex identified in the original SRB screen. 24 Thus, gene-specific signaling pathways that contribute to negative functions for the RNAPII-CTD are beginning to emerge.…”

“…2 ). 23 However, thus far, not all gene expression alterations associated with CTD truncation mutants are recapitulated in strains with CTD sequence alterations, 23,27 indicating that CTD length may also contribute to CTD function independently of its effect on CTD phosphorylation. On its own, CTD sequence is also important for function, as illustrated in mammals, where CTDs composed entirely of non-consensus repeats are unable to support viability.…”