Abstract: encodes an RNA (crRNA), consisting of a guide RNA (gRNA) and transactivating CRISPR RNA parts. A processed crRNA fragment is incorporated into the Cas9 protein, guiding it to the target DNA, where the Cas9 nuclease introduces a double-strand break9,10. The CRISPR-Cas system has been successfully used in human induced pluripotent stem cells, mice, zebrafish and flies, among other organisms, to disrupt gene function. Here we describe E-CRISP, a web application to design gRNA sequences (Fig. 1a). It provides flexible output and experimentoriented design parameters, enabling design of multiple libraries and thereby systematic analysis of the influence of different parameters. E-CRISP identifies target sequences complementary to the gRNA ending in a 3ʹ protospacer-adjacent motif (PAM), N(G or A)G, which is required for the recruited Cas9 nuclease to cut the DNA double strand. E-CRISP uses a fast indexing approach to find binding sites and a binary interval tree for rapid annotation of putative gRNA target sites (Supplementary Note 1). Using these algorithms, it is feasible to create genome-scale libraries for several organisms in a few hours. For instance, to design a library covering the Drosophila melanogaster genome requires less than 1 h (Supplementary Fig. 1 and Supplementary Table 1). Off-target effects and target-site homology are evaluated by E-CRISP using the alignment program Bowtie2 (Supplementary Note 2). Designs are shown in the output if the number of offtargets does not exceed a user-specified threshold. If more than one design is found targeting a desired locus, designs are ranked according to on-target specificity and number of off-targets. E-CRISP can also be used to reevaluate CRISPR constructs for onor off-target sites and targeted genomic loci. As an example, we searched for designs to target let-7 for gene disruption in zebrafish, fly, worm and human (Fig. 1b). We found at least one gRNA design per locus. In worm, fly and human, the cuts are located at the site that is transformed to mature microRNA and thus should lead to mutations blocking its proper function. In zebrafish the cut is located in the predicted hairpin structure. E-CRISP is available for twelve organisms and can be easily extended. E-CRISP will help to further develop and deploy the acKnoWLedGments This work was supported by the Wellcome Trust through a Senior Research Fellowship to J.R. (084229), a core grant to the Wellcome Trust Centre for Cell Biology (092076), a European Research Council grant (233457) to M.T., a Genome Québec International Recruitment Award to M.T. and a Canada Research Chair in Systems and Synthetic Biology to M.T.
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