Mutperiod: Analysis of Periodic Mutation Rates in Nucleosomes

Overview

Journal Comput Struct Biotechnol J

Specialty Biotechnology

Date 2021 Sep 16

PMID 34527191

Citations 3

Authors

Benjamin Morledge-Hampton

John J Wyrick

Affiliations

Soon will be listed here.

Abstract

Nucleosomes modulate DNA damage and repair, resulting in periodic mutation rates in nucleosomal DNA. Previous research has characterized these patterns in many sequenced tumor genomes; however, computational tools to identify and quantify these periodicities have not been developed for the broader scientific community. Here, we describe mutperiod, a Python and R based toolset that quantifies nucleosome mutational periodicities and compares them across different genetic and cellular backgrounds. We use mutperiod to demonstrate that DNA mismatch repair contributes to the nucleosome mutational periodicity observed in esophageal adenocarcinomas, and that the strength of this mutational periodicity varies in different chromatin states.

Citing Articles

Ultraviolet damage and repair maps in reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency.

Morledge-Hampton B, Selvam K, Chauhan M, Goodman A, Goodman A, Wyrick J Genome Res. 2025; 35(2):257-267.

PMID: 39762049 PMC: 11874968. DOI: 10.1101/gr.279605.124.

DNA Repair in Nucleosomes: Insights from Histone Modifications and Mutants.

Selvam K, Wyrick J, Parra M Int J Mol Sci. 2024; 25(8).

PMID: 38673978 PMC: 11050016. DOI: 10.3390/ijms25084393.

Analysis of cytosine deamination events in excision repair sequencing reads reveals mechanisms of incision site selection in NER.

Morledge-Hampton B, Kalyanaraman A, Wyrick J Nucleic Acids Res. 2023; 52(4):1720-1735.

PMID: 38109317 PMC: 10899786. DOI: 10.1093/nar/gkad1195.

Genome-wide maps of rare and atypical UV photoproducts reveal distinct patterns of damage formation and mutagenesis in yeast chromatin.

Bohm K, Morledge-Hampton B, Stevison S, Mao P, Roberts S, Wyrick J Proc Natl Acad Sci U S A. 2023; 120(10):e2216907120.

PMID: 36853943 PMC: 10013872. DOI: 10.1073/pnas.2216907120.

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