dUTP incorporation into genomic DNA is linked to transcription in yeast

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Abstract
When eukaryotic cells are transcribing at a high rate, it has been noted that genomic stability suffers, and mutational events are elevated. In this work, Nayun Kim and Sue Jinks-Robertson show that in yeast, highly transcribed DNA accumulates sites lacking a purine or pyrimidine base due to the removal of misincorporated uracil. This finding suggests that the fidelity of DNA synthesis can be affected by the level of transcription, and provides indirect evidence for nucleotide pool compartmentalization within the nucleus. High transcription rates in eukaryotic cells are associated with genomic instability, resulting in increased numbers of mutational events. In yeast, highly transcribed DNA is now shown to accumulate apurinic/apyrimidinic sites due to the removal of uracil, suggesting that the fidelity of DNA synthesis can be affected by the level of transcription. Highly activated transcription is associated with eukaryotic genome instability, resulting in increased rates of mitotic recombination and mutagenesis. The association between high transcription and genome stability is probably due to a variety of factors including an enhanced accumulation of DNA damage, transcription-associated supercoiling, collision between replication forks and the transcription machinery, and the persistence of RNA–DNA hybrids1. In the case of transcription-associated mutagenesis, we previously showed that there is a direct proportionality between the level of transcription and the mutation rate in the yeast Saccharomyces cerevisiae2, and that the molecular nature of the mutations is affected by highly activated transcription2,3. Here we show that the accumulation of apurinic/apyrimidinic sites is greatly enhanced in highly transcribed yeast DNA. We further demonstrate that most apurinic/apyrimidinic sites in highly transcribed DNA are derived from the removal of uracil, the presence of which is linked to direct incorporation of dUTP in place of dTTP. These results show an unexpected relationship between transcription and the fidelity of DNA synthesis, and raise intriguing cell biological issues with regard to nucleotide pool compartmentalization.