Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration

Abstract

mRNA homeostasis is favored by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5' exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position.Accumulation of RNA pol II at 3' was also detected in other mRNA decay mutants.According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favoring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.

Mechanisms of cellular mRNA transcript homeostasis

“…latter (functional mRNA buffering in xrn1 mutants) is supported by more recent experiments using orthogonal techniques [57,58]. However, none of these studies measured cell size, and mRNA production was normalized to cell number (using spike-ins) rather than to total protein or mRNA content [57][58][59]. This is important because haploid xrn1 mutants have been reported to be among the top 5% of S. cerevisiae mutants by cell size [60].…”

Transcription feedback dynamics in the wake of cytoplasmic degradation shutdown

“…Mechanistically, they linked Xrn1 levels to a control over the transcript levels of a negative transcriptional regulator -Nrg1. Since then, other studies with Xrn1 knockout/knockdown exhibited various transcriptional effects (Begley et al, 2021;Blasco-Moreno et al, 2019;Chattopadhyay et al;van Dijk et al, 2011;Fischer et al, 2020;García-Martínez et al, 2021a;Medina et al, 2014). Similarly, the Ccr4-Not complex which is crucial for mRNA deadenylation and degradation was also implicated in transcription regulation (Collart, 2016;Collart and Struhl, 1994;Gupta et al, 2016;Slobodin et al, 2020).…”

The transcription factor Sfp1 imprints specific classes of mRNAs and links their synthesis to cytoplasmic decay

“…We named the latter cases "mRNA imprinting", because this binding imprints the mRNA fate (Choder, 2011;Dahan and Choder, 2013;Pérez-Ortín and Chávez, 2022;Goler-Baron, 2008;Harel-Sharvit, 2010). Although Rpb4 is a quintessential imprinted factor, it functions as a general factor that binds to numerous mRNAs (Garrido-Godino et al, 2021). Imprinting by a "classical" transcription factor (TF) that binds to specific promoters, thus regulating transcription by modulating the assembly of general transcription factors, including Pol II, is currently unknown.…”

“…Thus, Sfp1 can be considered as a backtracking regulator. Regulators that antagonize Pol II backtracking are Xrn1 (Begley et al, 2021, 2019; Fischer et al, 2020), Rpb4 (Fischer et al, 2020) and the-Ccr4-Not complex (Collart, 2016), which prevents backtracking in a manner that depends on its Rpb4 and Rpb7 subunits (Babbarwal et al, 2014; Kruk et al, 2011). Interestingly, backtracking and TFIIS recruitment in RP genes are not influenced by Xrn1, but are strongly affected by Ccr4 (Begley et al, 2019).…”