Transcription as source of genetic heterogeneity in budding yeast

Transcription presents challenges to genome stability both directly, by altering genome topology and exposing single-stranded DNA to chemical insults and nucleases, and indirectly by introducing potential obstacles to the DNA replication machinery. Such obstacles include the RNA polymerase holoenzyme itself, DNA bound regulatory factors, G-quadruplexes and RNA::DNA hybrid structures known as R-loops. Here we review the detrimental impacts of transcription on genome stability in budding yeast, as well as the mitigating effects of transcription-coupled DNA repair and of systems that maintain DNA replication fork processivity and integrity. We conclude that the impacts of transcription on DNA replication by the replisome must be very mild with little direct mutagenic outcome under normal conditions. However, transcription can significantly impair the fidelity of replication fork rescue mechanisms, particularly Break Induced Replication (BIR), which is used to restart collapsed replication forks when other means fail. This leads to de novo mutations, structural variation and extrachromosomal circular DNA formation that contribute to genetic heterogeneity. By re-analysing published datasets, we show that different classes of genes have different interactions with the replisome, and that highly transcribed environment dependant genes in S. cerevisiae tend to be located close to replication origins. We have previously implicated interactions between replication origins and BIR forks in adaptive transcription-induced copy number variation events, which indicates that environment dependent genes are preferentially located in genomic environments more prone to instability, particularly under replication stress.