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Impact of cancer mutational signatures on transcription factor motifs in the human genome

By Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann

Posted 21 Sep 2018
bioRxiv DOI: 10.1101/422386 (published DOI: 10.1186/s12920-019-0525-4)

Somatic mutations in cancer genomes occur through a variety of molecular mechanisms, which contribute to different mutational patterns. To summarize these, mutational signatures have been defined using a large number of cancer genomes, and related to distinct mutagenic processes. Each cancer genome can be compared to this reference dataset and its exposure to one or the other signature be determined. Given the very different mutational patterns of these signatures, we anticipate that they will have distinct impact on genomic elements, in particular motifs for transcription factor binding sites (TFBS). In this work, we build the link between mutational signatures and TFBS motif alterations. We investigated and computed the theoretical impact of mutational signatures on 512 TFBS motifs, hence translating the trinucleotide mutation frequencies of the signatures into alteration frequencies of specific TFBS motifs, leading either to creation of disruption of these motifs. We further build a theoretical prediction of the alteration patterns for different cancer types based on the exposure of these cancer types to the mutation signatures. For certain motifs, a high correlation is observed between the TFBS motif creation and disruption events related to the information content of the motif. Our results show that the mutational signatures have different impact on the binding motifs of transcription factors and that for certain high complexity motifs there is a strong correlation between creation and disruption, related to the information content of the motif. This study represents a background estimation of the alterations due purely to mutational signatures in the absence of additional contributions, e.g. from evolutionary processes.

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