Identification of high-efficiency 3'GG gRNA motifs in indexed FASTA files with ngg2 [post]

Elisha D Roberson
2015 PeerJ Preprints  
CRISPR/Cas9 is emerging as one of the most used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3'GG motif, which substantially increases the efficiency of editing at all sites tested. Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a python command-line tool, ngg2,
more » ... -line tool, ngg2, to identify 3'GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six genomes: Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, and Homo sapiens. I identified more than 24 million single match 3'GG motifs in these reference genomes. Greater than 87% of all protein coding genes in the six reference genomes had at least one overlapping unique 3'GG gRNA site. In particular, more than 96% of mouse and 99% of human protein coding genes have at least one unique, overlapping 3'GG gRNA. These identified sites can be used as a starting point in gRNA design, and the ngg2 tool provides an important ability to identify high-efficiency editing sites in non-model species.
doi:10.7287/peerj.preprints.969v1 dblp:journals/peerjpre/Roberson15 fatcat:vj2gnikmm5em5ar4jixjrf4nvm