Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila.
We and others recently demonstrated that the readily programmable CRISPR/Cas9 system can be used to edit the Drosophila genome. However, most applications to date have relied on aberrant DNA repair to stochastically generate frameshifting indels and adoption has been limited by a lack of tools for efficient identification of targeted events. Here we report optimized tools and techniques for expanded application of the CRISPR/Cas9 system in Drosophila through homology-directed repair (HDR) with double-stranded DNA (dsDNA) donor templates that facilitate complex genome engineering through the precise incorporation of large DNA sequences, including screenable markers. Using these donors, we demonstrate the replacement of a gene with exogenous sequences and the generation of a conditional allele. To optimize efficiency and specificity, we generated transgenic flies that express Cas9 in the germline and directly compared HDR and off-target cleavage rates of different approaches for delivering CRISPR components. We also investigated HDR efficiency in a mutant background previously demonstrated to bias DNA repair toward HDR. Finally, we developed a web-based tool that identifies CRISPR target sites and evaluates their potential for off-target cleavage using empirically rooted rules. Overall, we have found that injection of a dsDNA donor and guide RNA-encoding plasmids into vasa-Cas9 flies yields the highest efficiency HDR and that target sites can be selected to avoid off-target mutations. Efficient and specific CRISPR/Cas9-mediated HDR opens the door to a broad array of complex genome modifications and greatly expands the utility of CRISPR technology for Drosophila research.
Genetics Training Program, University of Wisconsin, Madison, Wisconsin 53706.
Scott J
SJ
Gratz
Fiona P
FP
Ukken
C Dustin
CD
Rubinstein
Gene
G
Thiede
Laura K
LK
Donohue
Alexander M
AM
Cummings
Kate M
KM
O'Connor-Giles
D000818:Animals; D030801:Animals, Genetically Modified; D001426:Bacterial Proteins / Q000235:genetics*; D000076987:CRISPR-Associated Protein 9; D064130:CRISPR-Associated Proteins / Q000235:genetics / Q000378:metabolism*; D064113:CRISPR-Cas Systems; D053487:DEAD-box RNA Helicases / Q000235:genetics; D004247:DNA / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D004720:Endonucleases / Q000235:genetics*; D005260:Female; D000072669:Gene Editing / Q000379:methods*; D005854:Germ Cells / Q000378:metabolism; D008297:Male; D000094704:RNA, Guide, CRISPR-Cas Systems / Q000378:metabolism; D059767:Recombinational DNA Repair
D001426:Bacterial Proteins; D064130:CRISPR-Associated Proteins; D029721:Drosophila Proteins; D000094704:RNA, Guide, CRISPR-Cas Systems; D004247:DNA; D000076987:CRISPR-Associated Protein 9; C000606107:Cas9 endonuclease Streptococcus pyogenes; D004720:Endonucleases; C088269:vas protein, Drosophila; D053487:DEAD-box RNA Helicases
CRISPR RNA; Cas9; Drosophila; genome engineering; homologous recombination