Whole Genome Sequencing of Mutation Accumulation Lines Reveals a Low Mutation Rate in the Social Amoeba Dictyostelium discoideum

Gene–gene or gene–drug interactions are typically quantified using fitness as a readout because the data are continuous and easily measured in high throughput. However, to what extent fitness captures the range of other phenotypes that show synergistic effects is usually unknown. UsingSaccharomyces cerevisiaeand focusing on a matrix of DNA repair mutants and genotoxic drugs, we quantify 76 gene–drug interactions based on both mutation rate and fitness and find that these parameters are not connected. Independent of fitness defects, we identified six cases of synthetic hypermutation, where the combined effect of the drug and mutant on mutation rate was greater than predicted. One example occurred when yeast lackingRAD1were exposed to cisplatin, and we characterized this interaction using whole-genome sequencing. Our sequencing results indicate mutagenesis by cisplatin inrad1Δ cells appeared to depend almost entirely on interstrand cross-links at GpCpN motifs. Interestingly, our data suggest that the following base on the template strand dictates the addition of the mutated base. This result differs from cisplatin mutation signatures in XPF-deficientCaenorhabditis elegansand supports a model in which translesion synthesis polymerases perform a slippage and realignment extension across from the damaged base. Accordingly, DNA polymerase ζ activity was essential for mutagenesis in cisplatin-treatedrad1Δ cells. Together these data reveal the potential to gain new mechanistic insights from nonfitness measures of gene–drug interactions and extend the use of mutation accumulation and whole-genome sequencing analysis to define DNA repair mechanisms.

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Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

Nature Genetics ◽

10.1038/ng.811 ◽

2011 ◽

Vol 43 (5) ◽

pp. 482-486 ◽

Cited By ~ 281

Author(s):

Christopher B Ford ◽

Philana Ling Lin ◽

Michael R Chase ◽

Rupal R Shah ◽

Oleg Iartchouk ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mutation Rate ◽

Latent Infection ◽

Whole Genome

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The Dynamics of Somatic Mutagenesis During Life in Humans

Frontiers in Aging ◽

10.3389/fragi.2021.802407 ◽

2021 ◽

Vol 2 ◽

Author(s):

Freek Manders ◽

Ruben van Boxtel ◽

Sjors Middelkamp

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Adult Life ◽

Mutation Accumulation ◽

Lineage Tracing ◽

The Body ◽

Mutation Rates ◽

Driver Mutations ◽

Whole Genome ◽

Normal Tissues

From conception to death, human cells accumulate somatic mutations in their genomes. These mutations can contribute to the development of cancer and non-malignant diseases and have also been associated with aging. Rapid technological developments in sequencing approaches in the last few years and their application to normal tissues have greatly advanced our knowledge about the accumulation of these mutations during healthy aging. Whole genome sequencing studies have revealed that there are significant differences in mutation burden and patterns across tissues, but also that the mutation rates within tissues are surprisingly constant during adult life. In contrast, recent lineage-tracing studies based on whole-genome sequencing have shown that the rate of mutation accumulation is strongly increased early in life before birth. These early mutations, which can be shared by many cells in the body, may have a large impact on development and the origin of somatic diseases. For example, cancer driver mutations can arise early in life, decades before the detection of the malignancy. Here, we review the recent insights in mutation accumulation and mutagenic processes in normal tissues. We compare mutagenesis early and later in life and discuss how mutation rates and patterns evolve during aging. Additionally, we outline the potential impact of these mutations on development, aging and disease.

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New complexities of SOS-induced “untargeted” mutagenesis in Escherichia coli as revealed by mutation accumulation and whole-genome sequencing

DNA Repair ◽

10.1016/j.dnarep.2020.102852 ◽

2020 ◽

Vol 90 ◽

pp. 102852

Author(s):

Brittany A. Niccum ◽

Christopher P. Coplen ◽

Heewook Lee ◽

Wazim Mohammed Ismail ◽

Haixu Tang ◽

...

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mutation Accumulation ◽

Whole Genome

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Synthetic hypermutation: gene-drug mutation rate synergy reveals a translesion synthesis mechanism

10.1101/086512 ◽

2016 ◽

Author(s):

Romulo Segovia ◽

Yaoqing Shen ◽

Scott A. Lujan ◽

Steven Jones ◽

Peter C. Stirling

Keyword(s):

Dna Repair ◽

Drug Interactions ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Mutation Rate ◽

Synergistic Effects ◽

Translesion Synthesis ◽

Whole Genome ◽

Sequencing Analysis ◽

Synthesis Mechanism

ABSTRACTGene-gene or gene-drug interactions are typically quantified using fitness as readout because the data is continuous and easily measured in high-throughput. However, to what extent fitness captures the range of other phenotypes that show synergistic effects is usually unknown. Using Saccharomyces cerevisiae, and focusing on a matrix of DNA repair mutants and genotoxic drugs, we quantify 76 gene-drug interactions based on both mutation rate and fitness and find that these parameters are not necessarily overlapping. Independent of fitness defects we identified six cases of synthetic hypermutation, where the combined effect of the drug and mutant on mutation rate was greater than predicted. One example occurred when yeast lacking RAD1 were exposed to cisplatin and we characterized this interaction using whole-genome sequencing. Our sequencing results indicate mutagenesis by cisplatin in rad1Δ cells appeared to depend almost entirely on interstrand crosslinks at GpCpN motifs. Interestingly, our data suggests that the 3’ base in these motifs templates the addition of the mutated base. This result differs from cisplatin mutation signatures in XPF-deficient C. elegans and supports a model in which translesion synthesis polymerases perform a slippage and realignment extension across from the damaged base. Accordingly, DNA polymerase ζ activity was essential for mutagenesis in cisplatin treated rad1Δ cells. Together these data reveal the potential to gain new mechanistic insights from non-fitness measures of gene-drug interactions and extend the use of mutation accumulation and whole-genome sequencing analysis to define DNA repair mechanisms.

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New complexities of SOS-induced “untargeted” mutagenesis in Escherichia coli as revealed by mutation accumulation and whole-genome sequencing

10.1101/2020.01.15.908301 ◽

2020 ◽

Author(s):

Brittany A. Niccum ◽

Christopher P. Coplen ◽

Heewook Lee ◽

Wazim Mohammed Ismail ◽

Haixu Tang ◽

...

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Sos Response ◽

Mutation Accumulation ◽

List Type ◽

Whole Genome ◽

Sequence Specificity ◽

Wild Type ◽

Dna Strand

AbstractWhen its DNA is damaged, Escherichia coli induces the SOS response, which consists of about 40 genes that encode activities to repair or tolerate the damage. Certain alleles of the major SOS-control genes, recA and lexA, cause constitutive expression of the response, resulting in an increase in spontaneous mutations. These mutations, historically called “untargeted”, have been the subject of many previous studies. Here we re-examine SOS-induced mutagenesis using mutation accumulation followed by whole-genome sequencing (MA/WGS), which allows a detailed picture of the types of mutations induced as well as their sequence-specificity. Our results confirm previous findings that SOS expression specifically induces transversion base-pair substitutions, with rates averaging about 60-fold above wild-type levels. Surprisingly, the rates of G:C to C:G transversions, normally an extremely rare mutation, were induced an average of 160-fold above wild-type levels. The SOS-induced transversion showed strong sequence specificity, the most extreme of which was the G:C to C:G transversions, 60% of which occurred at the middle base of 5′GGC3′+5′GCC3′ sites although these sites represent only 8% of the G:C base pairs in the genome. SOS-induced transversions were also DNA strand biased, occurring, on average, 2- to 4- times more often when the purine was on the leading strand template and the pyrimidine on the lagging strand template than in the opposite orientation. However, the strand bias was also sequence specific, and even of reverse orientation at some sites. By eliminating constraints on the mutations that can be recovered, the MA/WGS protocol revealed new complexities to the nature of SOS “untargeted” mutations.HighlightsThe SOS response to DNA damage induces “untargeted” mutationsSOS-mutations are revealed by mutation accumulation and whole genome sequencingSOS-mutations are both sequence and DNA-strand biasedG:C to C:G transversions are particularly highly induced by SOSG:C to C:G transversions are extremely sequence and DNA-strand biased

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