Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease

Albino Bacolla, Nuri A Temiz, Ming Yi, Joseph Ivanic, Regina Z. Cer, Duncan E. Donohue, Edward V. Ball, Uma S. Mudunuri, Guliang Wang, Aklank Jain, Natalia Volfovsky, Brian T. Luke, Robert M. Stephens, David N. Cooper, Jack R. Collins, Karen M. Vasquez

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Single base substitutions constitute the most frequent type of human gene mutation and are a leading cause of cancer and inherited disease. These alterations occur non-randomly in DNA, being strongly influenced by the local nucleotide sequence context. However, the molecular mechanisms underlying such sequence context-dependent mutagenesis are not fully understood. Using bioinformatics, computational and molecular modeling analyses, we have determined the frequencies of mutation at G•C bp in the context of all 64 5′-NGNN-3′ motifs that contain the mutation at the second position. Twenty-four datasets were employed, comprising >530,000 somatic single base substitutions from 21 cancer genomes, >77,000 germline single-base substitutions causing or associated with human inherited disease and 16.7 million benign germline single-nucleotide variants. In several cancer types, the number of mutated motifs correlated both with the free energies of base stacking and the energies required for abstracting an electron from the target guanines (ionization potentials). Similar correlations were also evident for the pathological missense and nonsense germline mutations, but only when the target guanines were located on the non-transcribed DNA strand. Likewise, pathogenic splicing mutations predominantly affected positions in which a purine was located on the non-transcribed DNA strand. Novel candidate driver mutations and tissue-specific mutational patterns were also identified in the cancer datasets. We conclude that electron transfer reactions within the DNA molecule contribute to sequence context-dependent mutagenesis, involving both somatic driver and passenger mutations in cancer, as well as germline alterations causing or associated with inherited disease.

Original languageEnglish (US)
Article numbere1003816
JournalPLoS Genetics
Volume9
Issue number9
DOIs
StatePublished - Sep 1 2013

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guanine
Guanine
mutation
cancer
Mutation
neoplasms
germ cells
DNA
Neoplasms
Mutagenesis
substitution
Electrons
mutagenesis
Germ-Line Mutation
Nonsense Codon
Mutation Rate
Computational Biology
electron
bioinformatics
energy

Cite this

Bacolla, A., Temiz, N. A., Yi, M., Ivanic, J., Cer, R. Z., Donohue, D. E., ... Vasquez, K. M. (2013). Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease. PLoS Genetics, 9(9), [e1003816]. https://doi.org/10.1371/journal.pgen.1003816

Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease. / Bacolla, Albino; Temiz, Nuri A; Yi, Ming; Ivanic, Joseph; Cer, Regina Z.; Donohue, Duncan E.; Ball, Edward V.; Mudunuri, Uma S.; Wang, Guliang; Jain, Aklank; Volfovsky, Natalia; Luke, Brian T.; Stephens, Robert M.; Cooper, David N.; Collins, Jack R.; Vasquez, Karen M.

In: PLoS Genetics, Vol. 9, No. 9, e1003816, 01.09.2013.

Research output: Contribution to journalArticle

Bacolla, A, Temiz, NA, Yi, M, Ivanic, J, Cer, RZ, Donohue, DE, Ball, EV, Mudunuri, US, Wang, G, Jain, A, Volfovsky, N, Luke, BT, Stephens, RM, Cooper, DN, Collins, JR & Vasquez, KM 2013, 'Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease', PLoS Genetics, vol. 9, no. 9, e1003816. https://doi.org/10.1371/journal.pgen.1003816
Bacolla, Albino ; Temiz, Nuri A ; Yi, Ming ; Ivanic, Joseph ; Cer, Regina Z. ; Donohue, Duncan E. ; Ball, Edward V. ; Mudunuri, Uma S. ; Wang, Guliang ; Jain, Aklank ; Volfovsky, Natalia ; Luke, Brian T. ; Stephens, Robert M. ; Cooper, David N. ; Collins, Jack R. ; Vasquez, Karen M. / Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease. In: PLoS Genetics. 2013 ; Vol. 9, No. 9.
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