title: Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach.
abstract: We developed an in vivo library-on-library methodology to simultaneously assess single guide RNA (sgRNA) activity across ∼1,400 genomic loci. Assaying across multiple human cell types and end-processing enzymes as well as two Cas9 orthologs, we unraveled underlying nucleotide sequence and epigenetic parameters. Our results and software (http://crispr.med.harvard.edu/sgRNAScorer) enable improved design of reagents, shed light on mechanisms of genome targeting, and provide a generalizable framework to study nucleic acid-nucleic acid interactions and biochemistry in high throughput.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Raj
authors.initials: R
authors.lastname: Chari
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.
authors.forename: Prashant
authors.initials: P
authors.lastname: Mali
authors.affiliation: Scripps Institute of Oceanography, University of California, San Diego, La Jolla, California, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Moosburner
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.|Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA.
authors.forename: George M
authors.initials: GM
authors.lastname: Church
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D005818:Genetic Engineering / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D015698:Genomic Library; D006801:Humans; D012313:RNA / Q000235:genetics*; D012984:Software
chemical_list: D012313:RNA