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  • Review Article
  • Published:

Transcription as a source of genome instability

Nature Reviews Genetics volume 13, pages 204–214 (2012)Cite this article

Subjects

Key Points

  • Transcription is associated with elevated recombination and mutagenesis in bacteria and in eukaryotes and thereby alters the genetic landscape.

  • Concurrent transcription and replication of the same DNA template result in conflicts that lead to elevated chromosome fragility and recombination. In general, head-on collisions between the two machineries are more detrimental than co-directional collisions.

  • The formation of stable hybrids between the nascent RNA and its DNA template (R-loops) destabilizes the underlying template. Rapid engagement of the RNA discourages R-loop formation, but if formed, R-loops can be removed by RNase H or RNA–DNA helicases.

  • Transcription generates twin domains of positive and negative supercoiling, which are removed by topoisomerase 1 (Top1). The persistence of negative supercoils promotes R-loop formation.

  • Transcription facilitates the formation of non-B-DNA structures, which have been implicated in human trinucleotide repeat diseases.

  • Active genes suffer more DNA damage than inactive genes in bacteria and yeast, and damage preferentially accumulates on the non-transcribed strand. When DNA repair mechanisms are intact, most transcription-associated mutations in yeast are due to the activity of Top1.

  • Transcription in yeast can alter the base composition of the underlying DNA template, and uracil specifically replaces thymine.

Abstract

Alterations in genome sequence and structure contribute to somatic disease, affect the fitness of subsequent generations and drive evolutionary processes. The crucial roles of highly accurate replication and efficient repair in maintaining overall genome integrity are well-known, but the more localized stability costs that are associated with transcribing DNA into RNA molecules are less appreciated. Here we review the diverse ways in which the essential process of transcription alters the underlying DNA template and thereby modifies the genetic landscape.

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Figure 1: Co-directional and head-on orientations of RNA polymerase and the replisome.
Figure 2: Factors that promote and remove R-loops during transcription.
Figure 3: Non-B-DNA structures and genome instability.
Figure 4: Deducing the strand on which mutations arise.

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Acknowledgements

This work has been supported by grants from the US National Institutes of Health.

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  1. Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Nayun Kim & Sue Jinks-Robertson

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  1. Nayun Kim
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Glossary

Non-transcribed strand

(NTS). The NTS is complementary to the transcribed strand and has the same sequence as the RNA (except that it contains thymine instead of uracil); it is often referred to as the coding strand, whose sequence is given as standard.

Replisome

The multi-protein complex that contains all of the proteins that are required for DNA replication. This includes the DNA polymerases, factors that increase the processivity of DNA synthesis and a helicase to unwind duplex DNA.

Two-dimensional gels

These are used to visualize replication fork progression across a defined segment of DNA. DNA is separated by size in the first dimension and by shape in the second; the fragment of interest is visualized by Southern blot analysis. Linear fragments run on a diagonal; fragments that run off the diagonal correspond to replicating or branched molecules.

Chromatin immunoprecipitation followed by microarray

(ChIP–chip). DNA that interacts with a given protein is immunoprecipitated from cell extracts ('ChIP'). The precipitated DNA is labelled and hybridized to a microarray ('chip'), where signals above background reflect sequences preferentially immunoprecipitated with the protein of interest; it is used to map locations of protein–DNA interactions.

THO complex

A conserved protein complex that includes the proteins Tho2, Hpr1, Mft1 and Thp2 in yeast. It interacts with the TREX complex and functions in mRNA metabolism and export.

Transcription-coupled nucleotide excision repair

(TC-NER). TC-NER is a subpathway of the NER pathway that is initiated specifically in response to an RNA polymerase arrested by damage on the DNA template. The net effect is more efficient NER-directed repair of lesions on the transcribed than on the non-transcribed strand of active genes.

Reversion assays

Assays that start with a mutant allele, typically containing a change in a single base pair or the insertion or deletion of a single base pair, and that select for restoration of gene function. The change that restores gene function is usually limited to the position of the original mutation.

Forward mutations

Forward mutation assays select for loss of a gene function and can detect any change in the DNA sequence that inactivates the encoded product, which is usually a protein.

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Kim, N., Jinks-Robertson, S. Transcription as a source of genome instability. Nat Rev Genet 13, 204–214 (2012). https://doi.org/10.1038/nrg3152

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