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Surveying mutation density patterns around specific genomic features

Mutation density patterns reveal unique biological properties of specific genomic regions and shed light on the mechanisms of carcinogenesis. Although previous studies reported insightful mutation density patterns associated with certain genomic regions such as transcription start sites and DNA repl...

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Detalles Bibliográficos
Autores principales: Yu, Hui, Ness, Scott, Li, Chung-I, Bai, Yongsheng, Mao, Peng, Guo, Yan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9712630/
https://www.ncbi.nlm.nih.gov/pubmed/36100435
http://dx.doi.org/10.1101/gr.276770.122
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author Yu, Hui
Ness, Scott
Li, Chung-I
Bai, Yongsheng
Mao, Peng
Guo, Yan
author_facet Yu, Hui
Ness, Scott
Li, Chung-I
Bai, Yongsheng
Mao, Peng
Guo, Yan
author_sort Yu, Hui
collection PubMed
description Mutation density patterns reveal unique biological properties of specific genomic regions and shed light on the mechanisms of carcinogenesis. Although previous studies reported insightful mutation density patterns associated with certain genomic regions such as transcription start sites and DNA replication origins, a tool that can systematically investigate mutational spatial patterns is still lacking. Thus, we developed MutDens, a bioinformatic tool for comprehensive analysis of mutation density patterns around genomic features, namely, genomic positions, in humans and model species. By scanning the bidirectional vicinity regions of given positions, MutDens systematically characterizes the mutation density for single-base substitution mutational classes after adjusting for total mutation burden and local nucleotide proportion. Analysis results using MutDens not only verified the previously reported transcriptional strand bias around transcription start sites and replicative strand bias around DNA replication origins, but also identified novel mutation density patterns around other genomics features, such as enhancers and retrotransposon insertion polymorphism sites. To our knowledge, MutDens is the first tool that systematically calculates, examines, and compares mutation density patterns, thus providing a valuable avenue for investigating the mutational landscapes associated with important genomic features.
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spelling pubmed-97126302023-04-01 Surveying mutation density patterns around specific genomic features Yu, Hui Ness, Scott Li, Chung-I Bai, Yongsheng Mao, Peng Guo, Yan Genome Res Method Mutation density patterns reveal unique biological properties of specific genomic regions and shed light on the mechanisms of carcinogenesis. Although previous studies reported insightful mutation density patterns associated with certain genomic regions such as transcription start sites and DNA replication origins, a tool that can systematically investigate mutational spatial patterns is still lacking. Thus, we developed MutDens, a bioinformatic tool for comprehensive analysis of mutation density patterns around genomic features, namely, genomic positions, in humans and model species. By scanning the bidirectional vicinity regions of given positions, MutDens systematically characterizes the mutation density for single-base substitution mutational classes after adjusting for total mutation burden and local nucleotide proportion. Analysis results using MutDens not only verified the previously reported transcriptional strand bias around transcription start sites and replicative strand bias around DNA replication origins, but also identified novel mutation density patterns around other genomics features, such as enhancers and retrotransposon insertion polymorphism sites. To our knowledge, MutDens is the first tool that systematically calculates, examines, and compares mutation density patterns, thus providing a valuable avenue for investigating the mutational landscapes associated with important genomic features. Cold Spring Harbor Laboratory Press 2022-10 /pmc/articles/PMC9712630/ /pubmed/36100435 http://dx.doi.org/10.1101/gr.276770.122 Text en © 2022 Yu et al.; Published by Cold Spring Harbor Laboratory Press https://creativecommons.org/licenses/by-nc/4.0/This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) .
spellingShingle Method
Yu, Hui
Ness, Scott
Li, Chung-I
Bai, Yongsheng
Mao, Peng
Guo, Yan
Surveying mutation density patterns around specific genomic features
title Surveying mutation density patterns around specific genomic features
title_full Surveying mutation density patterns around specific genomic features
title_fullStr Surveying mutation density patterns around specific genomic features
title_full_unstemmed Surveying mutation density patterns around specific genomic features
title_short Surveying mutation density patterns around specific genomic features
title_sort surveying mutation density patterns around specific genomic features
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9712630/
https://www.ncbi.nlm.nih.gov/pubmed/36100435
http://dx.doi.org/10.1101/gr.276770.122
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