Reply to Chen and Zhang: On interpreting genome-wide trends from yeast mutation accumulation data

We are pleased to learn that our mutation accumulation (MA) dataset of 864 single nucleotide mutations (SNMs) in the budding yeast Saccharomyces cerevisiae (1) has attracted interest and is being applied to other analyses. MA mutations in large numbers can provide an unbiased picture of genome-wide patterns. One previously observed pattern is a positive correlation between transcription rate and mutation rate, inferred to be the result of transcription-associated mutagenesis (TAM) (2). In our paper, we used a conservative subset of 181 SNMs to analyze nascent transcription rate (TR) microarray data (3) and noted that the SNM rates observed were not significantly different between genes with varying TRs. Chen and …