Main text
At first sight, RNA polymerase II has evolved to function in a rather curious way with respect to genome integrity. Intuitively, we might expect the holoenzyme once loaded to simply follow the helical turns of the template strand, displacing histones and creating a single stranded bubble in a very localised region but causing minimal disruption to surrounding genome topology. This is not how RNA polymerase II operates: it passages DNA through the active site, creating positive supercoils ahead of the holoenzyme and negative supercoils behind that must be either resolved by topoisomerases or allowed to relax when the polymerase dissociates (Tsao et al., 1989). Quite how RNA polymerase achieves this remains unclear – even the bacterial RNA polymerase II working on a naked DNA can induce supercoiling (Janissen et al., 2023)  – and although this behaviour facilitates the release of the nascent RNA (which would otherwise become wound around the DNA) it also creates a set of vulnerabilities for mutation:
  1. Transcription requires the DNA helix to be transiently melted, and the single-stranded DNA (ssDNA) formed is more sensitive to chemical insults than dsDNA.
  2. Supercoiling around the polymerase must be relaxed by topoisomerases, which can be mutagenic when topoisomerase action is not completed.
  3. The transcription regulatory machinery and RNA polymerases must be removed to allow passage of replication forks.
  4. Negative supercoiling behind the polymerase enhances the formation of non-B DNA structures, such as G-quadruplexes and RNA:DNA hybrids called R-loops, which are considered to be a threat to genome stability.
Many of these vulnerabilities arise from interactions between DNA replication and direct or indirect outcomes of transcription. The replisome moves extremely rapidly and must traverse transcriptional units almost without pause to duplicate chromosomes sufficiently fast not to become the rate limiting step of cell division. Here we review the mechanisms by which transcription may induce DNA damage in the budding yeast S. cerevisiae , focusing particularly on interactions with DNA replication, and assess whether genome structure has evolved to enhance genetic heterogeneity at particular times and places by increasing vulnerability to transcription-induced genome instability.