Target-Specific Precision of CRISPR-Mediated Genome Editing

• Published in: Molecular cell 2019-02, Vol.73 (4), p.699-713.e6
• Main Authors: Chakrabarti, Anob M., Henser-Brownhill, Tristan, Monserrat, Josep, Poetsch, Anna R., Luscombe, Nicholas M., Scaffidi, Paola
• Format: Article
• Language: English
• Subjects: Cas9; Cell Proliferation; chromatin; Chromatin - genetics; Chromatin - metabolism; Chromatin Assembly and Disassembly; Clustered Regularly Interspaced Short Palindromic Repeats; CRISPR; CRISPR-Associated Protein 9 - genetics; CRISPR-Associated Protein 9 - metabolism; CRISPR-Cas Systems; DNA - genetics; DNA - metabolism; Gene Deletion; Gene Editing - methods; genome editing; HEK293 Cells; Hep G2 Cells; High-Throughput Nucleotide Sequencing; Humans; indel profiles; large-scale; Mutagenesis, Insertional; Nucleotide Motifs; precise; precision; predictability; RNA, Guide, CRISPR-Cas Systems - genetics; RNA, Guide, CRISPR-Cas Systems - metabolism; sgRNA
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2018.11.031

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. [Display omitted] •The outcome of CRISPR-mediated editing can be predicted•Not all target sites are edited in a predictable manner•The precision of DNA editing is mainly determined by the fourth nucleotide upstream of the PAM site•Chromatin states affect editing of imprecise, but not precise, target sites Chakrabarti, Henser-Brownhill, Monserrat et al. show that the genome-editing outcome can be predicted based on simple rules that mainly depend on the target site sequence. Since editing precision varies considerably across sites, careful selection of a predictable target is critical to induce a desired modification in a cell-type-independent manner.