Transcription as a source of genome instability

Abstract

Alterations in genome sequence and structure contribute to somatic disease, affect the fitness of subsequent generations and drive evolutionary processes. The crucial roles of highly accurate replication and efficient repair in maintaining overall genome integrity are well-known, but the more localized stability costs that are associated with transcribing DNA into RNA molecules are less appreciated. Here we review the diverse ways in which the essential process of transcription alters the underlying DNA template and thereby modifies the genetic landscape.

Figure 1. Co-directional and head-on orientations of RNA polymerase and the replisome

a | In the co-directional orientation, the transcribed strand (TS) is the leading-strand template for replication. b | In the head-on orientation, the TS is the lagging-strand template. Positive supercoils (+SCs) accumulate ahead of replisome; +SCs and negative supercoils (–SCs) accumulate ahead of and behind RNAP, respectively. Nascent DNA and RNA are indicated as solid and dashed red lines, respectively; arrowheads are at the 3′ ends of DNA strands. RNA polymerase is in blue and the replisome in yellow.

Figure 2. Factors that promote and remove R-loops during transcription

a | R-loop formation is favored by the negative supercoils that accumulate in the absence of Top1 and by naked RNA that fails to be engaged immediately after transcription. In bacteria, the coupling between transcription and translation prevents the accumulation of naked RNA. In eukaryotes, RNA is co-transcriptionally assembled into ribonucleoprotein particles for splicing and/or nuclear transport. R-loops can be actively unwound by an RNA:DNA helicase or the RNA component degraded by RNase H. b | Factors expected to affect the exposed nontranscribed strand within R-loops. DNA strands are in black, with 3′ ends indicated by the half-arrowheads; the RNA transcript is in red; and the large blue oval corresponds to RNA polymerase.

Figure 3. non-B DNA structures and genome instability

a | Representative non-B DNA structures are illustrated. b | Transcription through CAG•CTG repeats promotes the formation of slipped-strand structures, which subsequently stall RNA polymerase (RNAP) and lead to recruitment of the nucleotide excision repair (NER) machinery. Transcription-coupled NER removes the portion of the transcribed strand containing the RNAP-blocking hairpin; the resulting gap is filled in using the nontranscribed strand (NTS) as a template. Depending on the location of loops on the NTS relative to the removed hairpin, the repair event will either expand or contract the trinucleotide repeat.

Figure 4. Deducing the strand on which mutations arise

In the absence of uracil removal, deamination of C on the nontranscribed strand (NTS) leads to C > T mutations (note: by convention, DNA sequences are read from the NTS, which has the same sequence as the mRNA). In contrast, deamination of C on the transcribed strand results in G > T mutations.