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Measuring Microbial Mutation Rates with the Fluctuation Assay
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Measuring Microbial Mutation Rates with the Fluctuation Assay

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Mutperiod: Analysis of periodic mutation rates in nucleosomes

Benjamin Morledge-Hampton1, John J Wyrick1,2

  • 1School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA.

Computational and Structural Biotechnology Journal
|September 16, 2021
PubMed

Insights

We developed mutperiod, a computational tool to analyze DNA mutation patterns within nucleosomes. This tool reveals how DNA repair mechanisms influence mutation periodicity across various cellular environments.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Nucleosomes influence DNA damage and repair, leading to periodic mutation rates in DNA.
  • Existing methods for analyzing these patterns are not widely accessible to researchers.

Purpose of the Study:

  • To introduce mutperiod, a novel computational toolset for quantifying nucleosome mutational periodicities.
  • To enable comparisons of these periodicities across diverse genetic and cellular contexts.

Main Methods:

  • Development of mutperiod, a software toolset available in Python and R.
  • Application of mutperiod to analyze mutation patterns in tumor genomes.
  • Comparative analysis of mutational periodicities under different genetic and cellular conditions.

Main Results:

  • Demonstrated that DNA mismatch repair contributes to observed nucleosome mutational periodicity in esophageal adenocarcinomas.
  • Showed that the magnitude of nucleosome mutational periodicity is dependent on chromatin states.
  • Validated the utility of mutperiod for dissecting mutation patterns related to DNA repair and chromatin structure.

Conclusions:

  • mutperiod provides a valuable resource for the scientific community to study mutation periodicity.
  • The findings highlight the interplay between DNA repair, chromatin structure, and mutation patterns.
  • This work advances our understanding of genome instability in cancer.
Keywords:
DNA damageDNA repairEsophageal cancerMismatch repairMutationsNucleosomesSoftware

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