Cargando…
Mutperiod: Analysis of periodic mutation rates in nucleosomes
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 s...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Research Network of Computational and Structural Biotechnology
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8349767/ https://www.ncbi.nlm.nih.gov/pubmed/34527191 http://dx.doi.org/10.1016/j.csbj.2021.07.025 |
_version_ | 1783735627193253888 |
---|---|
author | Morledge-Hampton, Benjamin Wyrick, John J. |
author_facet | Morledge-Hampton, Benjamin Wyrick, John J. |
author_sort | Morledge-Hampton, Benjamin |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8349767 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Research Network of Computational and Structural Biotechnology |
record_format | MEDLINE/PubMed |
spelling | pubmed-83497672021-09-14 Mutperiod: Analysis of periodic mutation rates in nucleosomes Morledge-Hampton, Benjamin Wyrick, John J. Comput Struct Biotechnol J Research Article 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. Research Network of Computational and Structural Biotechnology 2021-07-26 /pmc/articles/PMC8349767/ /pubmed/34527191 http://dx.doi.org/10.1016/j.csbj.2021.07.025 Text en © 2021 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Research Article Morledge-Hampton, Benjamin Wyrick, John J. Mutperiod: Analysis of periodic mutation rates in nucleosomes |
title | Mutperiod: Analysis of periodic mutation rates in nucleosomes |
title_full | Mutperiod: Analysis of periodic mutation rates in nucleosomes |
title_fullStr | Mutperiod: Analysis of periodic mutation rates in nucleosomes |
title_full_unstemmed | Mutperiod: Analysis of periodic mutation rates in nucleosomes |
title_short | Mutperiod: Analysis of periodic mutation rates in nucleosomes |
title_sort | mutperiod: analysis of periodic mutation rates in nucleosomes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8349767/ https://www.ncbi.nlm.nih.gov/pubmed/34527191 http://dx.doi.org/10.1016/j.csbj.2021.07.025 |
work_keys_str_mv | AT morledgehamptonbenjamin mutperiodanalysisofperiodicmutationratesinnucleosomes AT wyrickjohnj mutperiodanalysisofperiodicmutationratesinnucleosomes |