The impediment to replication at tRNA genes inS. cerevisiaedoes not require tRNA transcription, and is facilitated by topoisomerases and Rad18-dependent repair pathways

Abstract

tRNA genes are widely studied sites of replication-fork pausing and genome instability in the budding yeast Saccharomyces cerevisiae. tRNAs are extremely highly transcribed and serve as constitutive condensin binding sites. tRNA transcription by RNA polymerase III has previously been identified as stimulating replication-fork pausing at tRNA genes, but the nature of the block to replication has not been incontrovertibly demonstrated. Here, we describe a systematic, genome-wide analysis of the contributions of candidates to replication-fork progression at tDNAs in yeast: transcription factor binding, transcription, topoisomerase activity, condensin-mediated clustering, and Rad18-dependent DNA repair. We show that an asymmetric block to replication is maintained even when tRNA transcription is abolished by depletion of one or more subunits of RNA polymerase III. By contrast, analogous depletion of the essential transcription factor TFIIIB removes the obstacle to replication.Therefore, our data suggest that the RNA polymerase III transcription complex itself represents an asymmetric obstacle to replication even in the absence of RNA synthesis. We additionally demonstrate that replication-fork progression past tRNA genes is unaffected by the global depletion of condensin from the nucleus, and can be stimulated by the removal of topoisomerases or Rad18dependent DNA repair pathways. genome instability at these sites are mitigated by the redundant activity of the Pif1-family helicases Pif1 and Rrm3 (Osmundson et al. 2017;Tran et al. 2017). Consistent with head-on replicationtranscription conflicts at tDNAs being deleterious, tDNAs show a strong bias towards the codirectional orientation in the yeast genome (Osmundson et al. 2017). An analogous statistical coorientation of replication and transcription is not observed for protein-coding genes in yeast (Raghuraman et al. 2001) but is prevalent in prokaryotes (Rocha and Danchin 2003) and has been described for both the C. elegans (Pourkarimi et al. 2016) and human replication programs (Petryk et al. 2016; Chen et al. 2019). Thus, replication-transcription conflicts can shape genome architecture and replication dynamics across biological kingdoms. Replication-transcription conflicts at both tDNAs and protein-coding genes are associated with genome instability in yeast (Prado and Aguilera 2005; Tran et al. 2017). Interestingly, replisome pausing and the onset of DNA damage at tDNAs appear to be mechanistically separable: co-oriented collisions in the absence of both Pif1 helicases impede a substantial fraction of replisomes (Osmundson et al. 2017; Tran et al. 2017), but only head-on conflicts lead to a dramatic increase in Rloop-dependent gross chromosomal rearrangements (Tran et al. 2017). Similarly to tDNAs, transcription-dependent mitotic recombination is strongly biased to the head-on orientation at a model protein-coding gene in yeast (Prado and Aguilera 2005). In humans, codirectional and head-on conflicts with RNA polymerase II both impede the replisome, but elicit di...