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      The Slit‐binding Ig1 domain is required for multiple axon guidance activities of Drosophila Robo2

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          Summary

          Drosophila Robo2 is a member of the evolutionarily conserved Roundabout (Robo) family of axon guidance receptors. Robo receptors signal midline repulsion in response to Slit ligands, which bind to the N‐terminal Ig1 domain in most family members. In the Drosophila embryonic ventral nerve cord, Robo1 and Robo2 signal Slit‐dependent midline repulsion, while Robo2 also regulates the medial‐lateral position of longitudinal axon pathways and acts non‐autonomously to promote midline crossing of commissural axons. While Robo2 signals midline repulsion in response to Slit, it is less clear whether Robo2's other activities are also Slit‐dependent. To determine which of Robo2's axon guidance roles depend on its Slit‐binding Ig1 domain, we used a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9‐based strategy to replace the endogenous robo2 gene with a robo2 variant lacking the Ig1 domain (robo2∆Ig1). We compare the expression and localization of Robo2∆Ig1 protein with full‐length Robo2 in embryonic neurons in vivo and examine its ability to substitute for Robo2 to mediate midline repulsion and lateral axon pathway formation. We find that the removal of the Ig1 domain from Robo2∆Ig1 disrupts both of these axon guidance activities. In addition, we find that the Ig1 domain of Robo2 is required for its proper subcellular localization in embryonic neurons, a role that is not shared by the Ig1 domain of Robo1. Finally, we report that although FasII‐positive lateral axons are misguided in embryos expressing Robo2∆Ig1, the axons that normally express Robo2 are correctly guided to the lateral zone, suggesting that Robo2 may guide lateral longitudinal axons through a cell non‐autonomous mechanism.

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          Fiji: an open-source platform for biological-image analysis.

          Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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            Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila.

            The type II clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system has emerged recently as a powerful method to manipulate the genomes of various organisms. Here, we report a toolbox for high-efficiency genome engineering of Drosophila melanogaster consisting of transgenic Cas9 lines and versatile guide RNA (gRNA) expression plasmids. Systematic evaluation reveals Cas9 lines with ubiquitous or germ-line-restricted patterns of activity. We also demonstrate differential activity of the same gRNA expressed from different U6 snRNA promoters, with the previously untested U6:3 promoter giving the most potent effect. An appropriate combination of Cas9 and gRNA allows targeting of essential and nonessential genes with transmission rates ranging from 25-100%. We also demonstrate that our optimized CRISPR/Cas tools can be used for offset nicking-based mutagenesis. Furthermore, in combination with oligonucleotide or long double-stranded donor templates, our reagents allow precise genome editing by homology-directed repair with rates that make selection markers unnecessary. Last, we demonstrate a novel application of CRISPR/Cas-mediated technology in revealing loss-of-function phenotypes in somatic cells following efficient biallelic targeting by Cas9 expressed in a ubiquitous or tissue-restricted manner. Our CRISPR/Cas tools will facilitate the rapid evaluation of mutant phenotypes of specific genes and the precise modification of the genome with single-nucleotide precision. Our results also pave the way for high-throughput genetic screening with CRISPR/Cas.
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              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.
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                Author and article information

                Contributors
                evanst@uark.edu
                Journal
                Genesis
                Genesis
                10.1002/(ISSN)1526-968X
                DVG
                Genesis (New York, N.y. : 2000)
                John Wiley & Sons, Inc. (Hoboken, USA )
                1526-954X
                1526-968X
                19 August 2021
                September 2021
                : 59
                : 9 ( doiID: 10.1002/dvg.v59.9 )
                : e23443
                Affiliations
                [ 1 ] Department of Biological Sciences University of Arkansas Fayetteville Arkansas USA
                [ 2 ] City of Houston Health Department University of Arkansas Houston Texas USA
                Author notes
                [*] [* ] Correspondence

                Timothy A. Evans, Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA.

                Email: evanst@ 123456uark.edu

                Author information
                https://orcid.org/0000-0002-2756-8064
                Article
                DVG23443
                10.1002/dvg.23443
                8446337
                34411419
                02a2f0bd-bdad-4cf8-9939-ca1cb4876f9a
                © 2021 The Authors. genesis published by Wiley Periodicals LLC.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 28 July 2021
                : 10 May 2021
                : 01 August 2021
                Page count
                Figures: 3, Tables: 0, Pages: 10, Words: 7752
                Funding
                Funded by: Arkansas Biosciences Institute , doi 10.13039/100008231;
                Funded by: National Institute of Neurological Disorders and Stroke , doi 10.13039/100000065;
                Award ID: R15NS098406
                Funded by: National Institutes of Health , doi 10.13039/100000002;
                Award ID: P40 OD‐018537
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                September 2021
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.0 mode:remove_FC converted:07.10.2022

                Molecular biology
                Molecular biology

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