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IGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity.

ABSTRACT: Genome engineering methods have advanced greatly with the development of programmable nucleases, but methods for quantifying on- and off-target cleavage sites and associated deletions remain nascent. Here, we report an improvement of the GUIDE-seq method, iGUIDE, which allows filtering of mispriming events to clarify the true cleavage signal. Using iGUIDE, we specify the locations of Cas9-guided cleavage for four guide RNAs, characterize associated deletions, and show that naturally occurring background DNA double-strand breaks are associated with open chromatin, gene dense regions, and chromosomal fragile sites. iGUIDE is available from https://github.com/cnobles/iGUIDE .

SUBMITTER: Nobles CL

PROVIDER: S-EPMC6337799 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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iGUIDE: an improved pipeline for analyzing CRISPR cleavage specificity.

Nobles Christopher L CL Reddy Shantan S Salas-McKee January J Liu Xiaojun X June Carl H CH Melenhorst J Joseph JJ Davis Megan M MM Zhao Yangbing Y Bushman Frederic D FD

Genome biology 20190117 1

Genome engineering methods have advanced greatly with the development of programmable nucleases, but methods for quantifying on- and off-target cleavage sites and associated deletions remain nascent. Here, we report an improvement of the GUIDE-seq method, iGUIDE, which allows filtering of mispriming events to clarify the true cleavage signal. Using iGUIDE, we specify the locations of Cas9-guided cleavage for four guide RNAs, characterize associated deletions, and show that naturally occurring ba ...[more]

PMID: 30654827

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