Transcription-associated mutational asymmetry in mammalian evolution

Although mutation is commonly thought of as a random process, evolutionary studies show that different types of nucleotide substitution occur with widely varying rates that presumably reflect biases intrinsic to mutation and repair mechanisms 1 , 2 , 3 , 4 . A strand asymmetry 5 , 6 , the occurrence of particular substitution types at higher rates than their complementary types, that is associated with DNA replication has been found in bacteria 7 and mitochondria 8 . A strand asymmetry that is associated with transcription and attributable to higher rates of cytosine deamination on the coding strand has been observed in enterobacteria 9 , 10 , 11 . Here, we describe a qualitatively different transcription-associated strand asymmetry in mammals, which may be a byproduct of transcription-coupled repair 12 in germline cells. This mutational asymmetry has acted over long periods of time to produce a compositional asymmetry, an excess of G+T over A+C on the coding strand, in most genes. The mutational and compositional asymmetries can be used to detect the orientations and approximate extents of transcribed regions.