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Target-specific precision of CRISPR-mediated genome editing
journal contributionposted on 2019-12-11, 18:01 authored by Anob M Chakrabarti, Tristan Henser-Brownhill, Josep Monserrat, Anna R Poetsch, Nicholas M Luscombe, Paola Scaffidi
The CRISPR-Cas9 system has successfully been adapted to edit the genome of various organisms. However, our ability to predict the editing outcome at specific sites is limited. Here, we examined indel profiles at over 1,000 genomic sites in human cells and uncovered general principles guiding CRISPR-mediated DNA editing. We find that precision of DNA editing (i.e., recurrence of a specific indel) varies considerably among sites, with some targets showing one highly preferred indel and others displaying numerous infrequent indels. Editing precision correlates with editing efficiency and a preference for single-nucleotide homologous insertions. Precise targets and editing outcome can be predicted based on simple rules that mainly depend on the fourth nucleotide upstream of the protospacer adjacent motif (PAM). Indel profiles are robust, but they can be influenced by chromatin features. Our findings have important implications for clinical applications of CRISPR technology and reveal general patterns of broken end joining that can provide insights into DNA repair mechanisms.
CRISPRCas9chromatingenome editingindel profileslarge-scalepreciseprecisionpredictabilitysgRNACRISPR-Associated Protein 9CRISPR-Cas SystemsCell ProliferationChromatinChromatin Assembly and DisassemblyClustered Regularly Interspaced Short Palindromic RepeatsDNAGene DeletionGene EditingHEK293 CellsHep G2 CellsHigh-Throughput Nucleotide SequencingHumansMutagenesis, InsertionalNucleotide MotifsRNA, GuideScaffidi FC001152Luscombe FC001110AS-ackCB-ack06 Biological Sciences11 Medical and Health SciencesDevelopmental Biology