In quiescent cells, an elongating RNAP is likely to encounter a DNA lesion on the template
strand of actively transcribed genes frequently, which could result in either blockage of
RNAP elongation or bypass of the lesion by the transcriptional machinery. Stalling or
blockage of the RNAP at a lesion site activates the transcription-coupled repair (TCR)
pathway (Box 1), which is a sub-pathway of the nucleotide excision repair (NER) pathway
that is dedicated to the elimination of DNA damage from the transcribed strand of a gene
(reviewed in24, 25). However, not all DNA lesions have the ability to stall or block an
elongating transcription complex and such lesions, having modified pairing properties, are
readily bypassed by RNAP with ribonucleotide misincorporation which can result in the
generation of mutant transcripts with a specific codon-specificity change (reviewed in26, 27).