Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli. Lee, H., Doak, T., G., Popodi, E., Foster, P., L., & Tang, H. Nucleic Acids Research, 44(15):7109-7119, Oxford University Press, 2016.
Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli [link]Website  doi  abstract   bibtex   
A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 × 10-4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 × 10-5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS1, IS2, IS5 and IS186. Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS186 target-sites, 5′-GGGG(N6/N7)CCCC-3′. We also detected 48 long deletions not involving IS elements. © 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
@article{
 title = {Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli},
 type = {article},
 year = {2016},
 keywords = {Article; bacterial genome; controlled study; DNA f,Bacterial; Mutagenesis,Base Sequence; DNA Transposable Elements; Escheri,Insertional,Molecular; Genome,transposon},
 pages = {7109-7119},
 volume = {44},
 websites = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84988377984&doi=10.1093%2Fnar%2Fgkw647&partnerID=40&md5=8bf10db5b54055c6f322feff9d7a4dc2},
 publisher = {Oxford University Press},
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 abstract = {A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 × 10-4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 × 10-5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS1, IS2, IS5 and IS186. Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS186 target-sites, 5′-GGGG(N6/N7)CCCC-3′. We also detected 48 long deletions not involving IS elements. © 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.},
 bibtype = {article},
 author = {Lee, H and Doak, T G and Popodi, E and Foster, P L and Tang, H},
 doi = {10.1093/nar/gkw647},
 journal = {Nucleic Acids Research},
 number = {15}
}
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