Letter | Published:

The nature of mutations induced by replication–transcription collisions

Nature volume 535, pages 178181 (07 July 2016) | Download Citation

Abstract

The DNA replication and transcription machineries share a common DNA template and thus can collide with each other co-directionally or head-on1,2. Replication–transcription collisions can cause replication fork arrest, premature transcription termination, DNA breaks, and recombination intermediates threatening genome integrity1,2,3,4,5,6,7,8,9,10. Collisions may also trigger mutations, which are major contributors to genetic disease and evolution5,7,11. However, the nature and mechanisms of collision-induced mutagenesis remain poorly understood. Here we reveal the genetic consequences of replication–transcription collisions in actively dividing bacteria to be two classes of mutations: duplications/deletions and base substitutions in promoters. Both signatures are highly deleterious but are distinct from the previously well-characterized base substitutions in the coding sequence. Duplications/deletions are probably caused by replication stalling events that are triggered by collisions; their distribution patterns are consistent with where the fork first encounters a transcription complex upon entering a transcription unit. Promoter substitutions result mostly from head-on collisions and frequently occur at a nucleotide that is conserved in promoters recognized by the major σ factor in bacteria. This substitution is generated via adenine deamination on the template strand in the promoter open complex, as a consequence of head-on replication perturbing transcription initiation. We conclude that replication–transcription collisions induce distinct mutation signatures by antagonizing replication and transcription, not only in coding sequences but also in gene regulatory elements.

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Acknowledgements

We thank E. Robleto, R. Yasbin and L. Simmons for strains, M. Cox, R. Gourse, C. Hittinger, R. Landick, K. Wasserman, C. Gross, M. Laub, S. Rosenberg, L. Simmons and the Wang laboratory for discussions and comments on the manuscript. This work was supported by the National Institutes of Health Director’s New Innovator Award DP2OD004433 to J.D.W.

Author information

Author notes

    • T. Sabari Sankar
    •  & Brigitta D. Wastuwidyaningtyas

    These authors contributed equally to this work.

Affiliations

  1. Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA

    • T. Sabari Sankar
    • , Yuexin Dong
    •  & Jue D. Wang
  2. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA

    • T. Sabari Sankar
    • , Brigitta D. Wastuwidyaningtyas
    • , Sarah A. Lewis
    •  & Jue D. Wang

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Contributions

J.D.W. conceptualized the study. T.S.S., B.D.W. and J.D.W. designed the experiments. T.S.S. performed thyP3 fluctuation tests and sequencing of recA, yqjH, mutSL and adeC mutants, comparative genomic analyses, nitrous acid mutagenesis, competition assays and plating efficiency of mutants. B.D.W. developed the forward mutation assay, fluctuation tests and sequencing of wild-type strains, qRT–PCR, nalidixic acid fluctuation test, doubling time measurements and developed the restriction digest screening. Y.D. assisted the competition assay, plating efficiency and mutSL fluctuation tests. S.A.L. performed thyP3 fluctuation tests with B.D.W. T.S.S., B.D.W. and J.D.W. analysed the data and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jue D. Wang.

Reviewer Information Nature thanks S. Mirkin, E. Nudler and R. Pomerantz for their contribution to the peer review of this work.

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DOI

https://doi.org/10.1038/nature18316

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