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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... Full description

Journal Title: Scientific reports February 9, 2015, Vol.5, p.8333
Main Author: Chen, Wei
Other Authors: Zhang, Liqing
Format: Electronic Article Electronic Article
Language: English
Subjects:
DNA
ID: E-ISSN: 2045-2322 ; DOI: 2045-2322 ; DOI: 10.1038/srep08333
Link: http://search.proquest.com/docview/1653128660/?pq-origsite=primo
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title: The pattern of DNA cleavage intensity around indels.
format: Article
creator:
  • Chen, Wei
  • Zhang, Liqing
subjects:
  • Animals–Genetics
  • DNA–Genetics
  • DNA Mutational Analysis–Genetics
  • Humans–Genetics
  • Indel Mutation–Genetics
  • Mice–Genetics
  • Pan Troglodytes–Genetics
  • Repetitive Sequences, Nucleic Acid–Genetics
  • Species Specificity–Genetics
  • DNA
ispartof: Scientific reports, February 9, 2015, Vol.5, p.8333
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.
language: eng
source:
identifier: E-ISSN: 2045-2322 ; DOI: 2045-2322 ; DOI: 10.1038/srep08333
fulltext: fulltext
issn:
  • 20452322
  • 2045-2322
url: Link


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titleThe pattern of DNA cleavage intensity around indels.
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subjectAnimals–Genetics ; DNA–Genetics ; DNA Mutational Analysis–Genetics ; Humans–Genetics ; Indel Mutation–Genetics ; Mice–Genetics ; Pan Troglodytes–Genetics ; Repetitive Sequences, Nucleic Acid–Genetics ; Species Specificity–Genetics ; DNA
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descriptionIndels (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.
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