scholarly journals DNA mismatch repair and oligonucleotide end-protection promote base-pair substitution distal from a CRISPR/Cas9-induced DNA break

2018 ◽  
Vol 46 (6) ◽  
pp. 2945-2955 ◽  
Author(s):  
Tim Harmsen ◽  
Sjoerd Klaasen ◽  
Henri van de Vrugt ◽  
Hein te Riele
Keyword(s):  
Mismatch Repair ◽  
Base Pair ◽  
Dna Mismatch Repair ◽  
Dna Mismatch ◽  
Dna Break ◽  
Base Pair Substitution

scholarly journals Determinants of Base-Pair Substitution Patterns Revealed by Whole-Genome Sequencing of DNA Mismatch Repair DefectiveEscherichia coli

Genetics ◽  
2018 ◽  
Vol 209 (4) ◽  
pp. 1029-1042 ◽  
Author(s):  
Patricia L. Foster ◽  
Brittany A. Niccum ◽  
Ellen Popodi ◽  
Jesse P. Townes ◽  
Heewook Lee ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Mismatch Repair ◽  
Genome Sequencing ◽  
Base Pair ◽  
Dna Mismatch Repair ◽  
Whole Genome ◽  
Dna Mismatch ◽  
Base Pair Substitution

scholarly journals Determinants of base-pair substitution patterns revealed by whole-genome sequencing of DNA mismatch repair defectiveEscherichia coli

2018 ◽  
Author(s):  
Patricia L. Foster ◽  
Brittany A. Niccum ◽  
Ellen Popodi ◽  
Jesse P. Townes ◽  
Heewook Lee ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Mismatch Repair ◽  
Genome Sequencing ◽  
Base Pair ◽  
Whole Genome ◽  
Dna Mismatch ◽  
In The Wild ◽  
Leading Strand ◽  
Base Pair Substitution ◽  
Lagging Strand

ABSTRACTMismatch repair (MMR) is a major contributor to replication fidelity, but its impact varies with sequence context and the nature of the mismatch. Mutation accumulation experiments followed by whole-genome sequencing of MMR-defectiveE. colistrains yielded ≈30,000 base-pair substitutions, revealing mutational patterns across the entire chromosome. The base-pair substitution spectrum was dominated by A:T > G:C transitions, which occurred predominantly at the center base of 5′NAC3′+5′GTN3′ triplets. Surprisingly, growth on minimal medium or at low temperature attenuated these mutations. Mononucleotide runs were also hotspots for base-pair substitutions, and the rate at which these occurred increased with run length. Comparison with ≈2000 base-pair substitutions accumulated in MMR-proficient strains revealed that both kinds of hotspots appeared in the wild-type spectrum and so are likely to be sites of frequent replication errors. In MMR-defective strains transitions were strand biased, occurring twice as often when A and C rather than T and G were on the lagging-strand template. Loss of nucleotide diphosphate kinase increases the cellular concentration of dCTP, which resulted in increased rates of mutations due to misinsertion of C opposite A and T. In anmmr ndkdouble mutant strain, these mutations were more frequent when the template A and T were on the leading strand, suggesting that lagging-strand synthesis was more error-prone or less well corrected by proofreading than was leading strand synthesis.

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