The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4

Abstract

Co-transcriptional imprinting of mRNA by Rpb4 and Rpb7 subunits of RNA polymerase II (RNAPII) and by the Ccr4–Not complex conditions its post-transcriptional fate. In turn, mRNA degradation factors like Xrn1 are able to influence RNAPII-dependent transcription, making a feedback loop that contributes to mRNA homeostasis. In this work, we have used repressible yeast GAL genes to perform accurate measurements of transcription and mRNA degradation in a set of mutants. This genetic analysis uncovered a link from mRNA decay to transcription elongation. We combined this experimental approach with computational multi-agent modelling and tested different possibilities of Xrn1 and Ccr4 action in gene transcription. This double strategy brought us to conclude that both Xrn1–decaysome and Ccr4–Not regulate RNAPII elongation, and that they do it in parallel. We validated this conclusion measuring TFIIS genome-wide recruitment to elongating RNAPII. We found that xrn1Δ and ccr4Δ exhibited very different patterns of TFIIS versus RNAPII occupancy, which confirmed their distinct role in controlling transcription elongation. We also found that the relative influence of Xrn1 and Ccr4 is different in the genes encoding ribosomal proteins as compared to the rest of the genome.

Cytoplasmic mRNA decay factors modulate RNA polymerase II processivity in 5’ and 3’ gene regions in yeast

“…The simplest explanation is that different DFs differentially affect the initiation/elongation ratio by targeting initiation, elongation/backtracking, or both as demonstrated using our mathematical model. This is consistent with the recent report that Xrn1 and Ccr4 differentially regulate Pol II elongation; namely, whereas deletion of XRN 1 led to increased TFIIS-Pol II interaction, that of CCR 4 had the opposite effect (Begley et al 2019). Nonetheless, the exact mechanism remains to be determined.…”

“…Likewise, Dhh1, Pat1, and Lsm1 also interact with TFIIS both physically and genetically (Collins et al 2007; Costanzo et al 2010; Costanzo et al 2016; Dutta et al 2015; Kuzmin et al 2018; Miller et al 2018; Srivas et al 2016; Wilmes et al 2008). Recently, Xrn1 was shown to increase TFIIS recruitment to Pol II (Begley et al 2019), consistent with the role we assign to Xrn1 as a regulator of backtracking. All these observations provide outside credibility to our proposals.…”

“…3A, S6A, S6B). Based on mathematical modeling (see below), we interpret these results to mean that the deletion of any one of these mRNA decay factors results in defective transcription initiation in addition to previous findings that XRN 1 deletion leads to defective elongation (Haimovich et al 2013; Begley et al 2019). In contrast, deletions of CCR 4 and RPB 4 resulted in sharper Pol II peaks.…”

Feedback to the central dogma: cytoplasmic mRNA decay and transcription are interdependent processes

“…Several recent reports further implicate Xrn1 in transcription elongation at yeast genes. In a Dxrn1 strain less elongating Pol II was found at GAL loci by transcriptional run on (Begley et al 2019) and genome wide by Native Elongating Transcript (NET) sequencing (Fischer et al 2019). Furthermore, the Dxrn1 strain showed increased recruitment of the Pol II release factor TFIIS to the body of the GAL genes (Begley et al 2019).…”

“…demonstrates reduced elongating Pol II and reduced Pol II speed at GAL genes in an Dxrn1 strain (Begley et al 2019). Each of these studies implicate Xrn1 in the transcriptional response to alterations in global mRNA stability, although the basis for differing transcriptional effects in the absence of Xrn1 is unclear.…”