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Nucleic Acids Res. 2016 Feb 29;44(4):1669-80. doi: 10.1093/nar/gkv1298. Epub 2015 Nov 24.

Genome-wide analysis of the specificity and mechanisms of replication infidelity driven by imbalanced dNTP pools.

Author information

1
Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
2
Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden.
3
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
4
Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden andrei.chabes@umu.se.

Abstract

The absolute and relative concentrations of the four dNTPs are key determinants of DNA replication fidelity, yet the consequences of altered dNTP pools on replication fidelity have not previously been investigated on a genome-wide scale. Here, we use deep sequencing to determine the types, rates and locations of uncorrected replication errors that accumulate in the nuclear genome of a mismatch repair-deficient diploid yeast strain with elevated dCTP and dTTP concentrations. These imbalanced dNTP pools promote replication errors in specific DNA sequence motifs suggesting increased misinsertion and increased mismatch extension at the expense of proofreading. Interestingly, substitution rates are similar for leading and lagging strand replication, but are higher in regions replicated late in S phase. Remarkably, the rate of single base deletions is preferentially increased in coding sequences and in short rather than long mononucleotides runs. Based on DNA sequence motifs, we propose two distinct mechanisms for generating single base deletions in vivo. Collectively, the results indicate that elevated dCTP and dTTP pools increase mismatch formation and decrease error correction across the nuclear genome, and most strongly increases mutation rates in coding and late replicating sequences.

PMID:
26609135
PMCID:
PMC4770217
DOI:
10.1093/nar/gkv1298
[Indexed for MEDLINE]
Free PMC Article

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