Signatures of TOP1 transcription-associated mutagenesis in cancer and germline

Martin A M Reijns, David A. Parry, Thomas C Williams, Ferran Nadeu, Rebecca L Hindshaw, Diana O Rios Szwed, Michael D. Nicholson, Paula Carroll, Shelagh Boyle, Romina Royo, Alex J Cornish, Hang Xiang, Kate Ridout, The Genomics England Research Consortium, Colorectal Cancer Domain UK 100,000 Genomes Project, Anna Schuh, Konrad Aden, Claire Palles, Elías Campo, Tatjana StankovicMartin S Taylor, Andrew P Jackson

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

The mutational landscape is shaped by many processes. Genic regions are vulnerable to mutation but are preferentially protected by transcription-coupled repair 1. In microorganisms, transcription has been demonstrated to be mutagenic 2,3; however, the impact of transcription-associated mutagenesis remains to be established in higher eukaryotes 4. Here we show that ID4-a cancer insertion-deletion (indel) mutation signature of unknown aetiology 5 characterized by short (2 to 5 base pair) deletions -is due to a transcription-associated mutagenesis process. We demonstrate that defective ribonucleotide excision repair in mammals is associated with the ID4 signature, with mutations occurring at a TNT sequence motif, implicating topoisomerase 1 (TOP1) activity at sites of genome-embedded ribonucleotides as a mechanistic basis. Such TOP1-mediated deletions occur somatically in cancer, and the ID-TOP1 signature is also found in physiological settings, contributing to genic de novo indel mutations in the germline. Thus, although topoisomerases protect against genome instability by relieving topological stress 6, their activity may also be an important source of mutations in the human genome.

Original languageEnglish
Pages (from-to)623-631
Publication statusPublished - 9 Feb 2022


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