Identification of high-efficiency 3’GG gRNA motifs in indexed FASTA files with ngg2

Abstract

15CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in 16 organisms ranging from bacteria to human cells. However, the efficiency of editing 17 varies tremendously site-to-site. A recent report identified a novel motif, called the 18 3'GG motif, which substantially increases the efficiency of editing at all sites tested in C. 19 elegans. Furthermore, they highlighted that previously published gRNAs with high 20 editing efficiency also had this motif. I designed a python command-line tool, ngg2, to 21 identify 3'GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened 22 for these motifs in six model genomes: Saccharomyces cerevisiae, Caenorhabditis elegans, 23 Drosophila melanogaster, Danio rerio, Mus musculus, and Homo sapiens. I also scanned the 24 genomes of pig (Sus scrofa) and African elephant (Loxodonta africana) to demonstrate the 25 utility in non-model organisms. I identified more than 60 million single match 3'GG 26 motifs in these genomes. Greater than 61% of all protein coding genes in the reference 27 genomes had at least one unique 3'GG gRNA site overlapping an exon. In particular, 28 more than 96% of mouse and 93% of human protein coding genes have at least one 29 unique, overlapping 3'GG gRNA. These identified sites can be used as a starting point 30

Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files

“…Inspired by previous work to identify a specific subset of CRISPR/ Cas9 sites (Roberson, 2015), my goal for motif scraper was to instead develop a more general purpose motif searching tool that would have broader use. Motif scraper fills this annotation gap by allowing for the specification degenerate sequence motifs and reporting the location and composition of all matches in a FASTA file, which could be a personal genome, a reference genome, or a set of genomic slices, such as all the 3 0 UTRs of protein coding genes.…”