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The pattern of DNA cleavage intensity around indels
Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321175/ https://www.ncbi.nlm.nih.gov/pubmed/25660536 http://dx.doi.org/10.1038/srep08333 |
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author | Chen, Wei Zhang, Liqing |
author_facet | Chen, Wei Zhang, Liqing |
author_sort | Chen, Wei |
collection | PubMed |
description | Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small human and mouse germline indels, 16,742 human somatic indels, 10,599 large human insertions, and 5,822 large chimpanzee insertions and systematically analyzed the patterns of DNA cleavage intensities in the 200 base pair regions surrounding these indels. Our results show that DNA cleavage intensities close to the start and end points of indels are significantly lower than other regions, for both small human germline and somatic indels and also for mouse small indels. Compared to small indels, the patterns of DNA cleavage intensity around large indels are more complex, and there are two low intensity regions near each end of the indels that are approximately 13 bp apart from each other. Detailed analyses of a subset of indels show that there is slight difference in cleavage intensity distribution between insertion indels and deletion indels that could be contributed by their respective enrichment of different repetitive elements. These results will provide new insight into indel generation mechanisms. |
format | Online Article Text |
id | pubmed-4321175 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-43211752015-02-12 The pattern of DNA cleavage intensity around indels Chen, Wei Zhang, Liqing Sci Rep Article Indels (insertions and deletions) are the second most common form of genetic variations in the eukaryotic genomes and are responsible for a multitude of genetic diseases. Despite its significance, detailed molecular mechanisms for indel generation are still unclear. Here we examined 2,656,597 small human and mouse germline indels, 16,742 human somatic indels, 10,599 large human insertions, and 5,822 large chimpanzee insertions and systematically analyzed the patterns of DNA cleavage intensities in the 200 base pair regions surrounding these indels. Our results show that DNA cleavage intensities close to the start and end points of indels are significantly lower than other regions, for both small human germline and somatic indels and also for mouse small indels. Compared to small indels, the patterns of DNA cleavage intensity around large indels are more complex, and there are two low intensity regions near each end of the indels that are approximately 13 bp apart from each other. Detailed analyses of a subset of indels show that there is slight difference in cleavage intensity distribution between insertion indels and deletion indels that could be contributed by their respective enrichment of different repetitive elements. These results will provide new insight into indel generation mechanisms. Nature Publishing Group 2015-02-09 /pmc/articles/PMC4321175/ /pubmed/25660536 http://dx.doi.org/10.1038/srep08333 Text en Copyright © 2015, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by-nc-nd/4.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/4.0/ |
spellingShingle | Article Chen, Wei Zhang, Liqing The pattern of DNA cleavage intensity around indels |
title | The pattern of DNA cleavage intensity around indels |
title_full | The pattern of DNA cleavage intensity around indels |
title_fullStr | The pattern of DNA cleavage intensity around indels |
title_full_unstemmed | The pattern of DNA cleavage intensity around indels |
title_short | The pattern of DNA cleavage intensity around indels |
title_sort | pattern of dna cleavage intensity around indels |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4321175/ https://www.ncbi.nlm.nih.gov/pubmed/25660536 http://dx.doi.org/10.1038/srep08333 |
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