Expression-dependent but strand-independent synonymous single-nucleotide polymorphism in the Escherichia coli chromosome

BackgroundMutation is thought to arise mainly during replication, though transcription is also known to be mutagenic. Considering the recent reports regarding genome-wide transcription-induced mutagenesis, a distinct demonstration of specific mutation being replication-dependent and/or transcription-dependent in genomes is yet to be established. Here, we studied synonymous single-nucleotide polymorphisms (SNPs) in 2091 individual coding sequences (CDS) in the leading strand (LeS) and the lagging strand (LaS) of the Escherichia coli chromosome by comparing across 157 strains. The frequencies of complementary transitions (ti) and complementary transversions (tv) were compared in each CDS to assess parity violation in the strands. ResultsThe C[->]T and G[->]A exhibited the maximum frequency as well as the most prominent strand inequality as these tis were influenced both by the strands as well as by the expression. Interestingly, inequality between T[->]C and A[->]G was expression-dependent but strand-independent. A[->]T and G[->]T tvs were universally more frequent than their complementary T[->]A and C[->]A tvs, respectively. ConclusionsOur study demonstrates strand-independent but expression-dependent synonymous SNP inequality in CDS, supporting the role of transcription-induced mutagenesis contributing to strand inequality in the E. coli chromosome.