The pattern of DNA cleavage intensity around indels

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dc.contributor.authorChen, Weien
dc.contributor.authorZhang, Liqingen
dc.contributor.departmentComputer Scienceen
dc.date.accessioned2019-01-29T14:22:19Zen
dc.date.available2019-01-29T14:22:19Zen
dc.date.issued2015-02-09en
dc.description.abstractIndels (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.en
dc.description.notesThe authors would like to thank Prof. John McDonald for providing the data of large indels in Human and Chimpanzee genomes. This work was supported by the National Nature Scientific Foundation of China (No. 61100092) and the Nature Scientific Foundation of Hebei Province (No.C2013209105).en
dc.description.sponsorshipNational Nature Scientific Foundation of China [61100092]; Nature Scientific Foundation of Hebei Province [C2013209105]en
dc.format.extent8en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1038/srep08333en
dc.identifier.issn2045-2322en
dc.identifier.other8333en
dc.identifier.pmid25660536en
dc.identifier.urihttp://hdl.handle.net/10919/87067en
dc.identifier.volume5en
dc.language.isoen_USen
dc.publisherSpringer Natureen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjecthydroxyl radical cleavageen
dc.subjectsequencing dataen
dc.subjectinsertion-deletionen
dc.subjectgenetic-variationen
dc.subjectgenome evolutionen
dc.subjectpredictionen
dc.subjectreplicationen
dc.subjectmutationsen
dc.subjectrecombinationen
dc.subjectconstructionen
dc.titleThe pattern of DNA cleavage intensity around indelsen
dc.title.serialScientific Reportsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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