Use of high throughput sequencing to observe genome dynamics at a single cell level

With the advent of high-throughput sequencing technology, it becomes possible to directly analyze genetic variability in a genome-wide fashion. We sequenced several genomes of Escherichia coli from colonies obtained after treatment of cells with the mutagen EMS, and observed a strikingly nonrandom distribution of the induced mutations. These include long stretches of exclusively G to A or C to T transitions along the bacterial genome and orders of magnitude differences in mutation density between different areas of the genome. The first feature of the observed patterns, albeit somewhat surprising, is consistent with the elementary notions of how the mutations are produced from mutagenic lesions and then segregate from each other as a result of semiconservative DNA replication and recombination. The second feature, termed here ‘mutation bunching’, is reminiscent of the phenomenon of transcription bursts and could reflect the stochasticity in the molecular processes responsible for the mutation repair and fixation. Our results demonstrate how analysis of the molecular records left in the genomes of the descendants of an individual mutagenized cell allows for genome-scale observations of fixation and segregation of mutations, as well as recombination events, in the single genome of their progenitor. It also paves the way for independent verification of the traditional assumptions that underlie studies of genetic variability.