Editing Transgenic DNA Components by Inducible Gene Replacement in Drosophila melanogaster

Abstract

Gene conversions occur when genomic double-strand DNA breaks (DSBs) trigger unidirectional transfer of genetic material from a homologous template sequence. Exogenous or mutated sequence can be introduced through this homology-directed repair (HDR). We leveraged gene conversion to develop a method for genomic editing of existing transgenic insertions in Drosophila melanogaster. The clustered regularly-interspaced palindromic repeats (CRISPR)/Cas9 system is used in the homology assisted CRISPR knock-in (HACK) method to induce DSBs in a GAL4 transgene, which is repaired by a single-genomic transgenic construct containing GAL4 homologous sequences flanking a T2A-QF2 cassette. With two crosses, this technique converts existing GAL4 lines, including enhancer traps, into functional QF2 expressing lines. We used HACK to convert the most commonly-used GAL4 lines (labeling tissues such as neurons, fat, glia, muscle, and hemocytes) to QF2 lines. We also identified regions of the genome that exhibited differential efficiencies of HDR. The HACK technique is robust and readily adaptable for targeting and replacement of other genomic sequences, and could be a useful approach to repurpose existing transgenes as new genetic reagents become available.KEYWORDS gene conversion; CRISPR/Cas9; homology-directed repair; genomic engineering; updating transgenes D OUBLE-strand DNA breaks (DSBs) in genomic DNA are potentially lethal to the cell as they are substrates for genomic rearrangements. Two major endogenous repair mechanisms exist to resolve such DNA damage. Nonhomologous end-joining (NHEJ) involves ligation of the damaged ends and often results in small insertion/deletion (indel) mutations at the site of the DSB (Lieber 2010). This causes frameshifting and the expression of mutated or nonfunctional protein. In contrast, homologous recombination (HR) uses a homologous template for repair to preserve genomic integrity. Gene conversion is one form of HR and involves unidirectional transfer of genetic material from a donor sequence to a highly homologous target (Engels et al. 1990;Gloor et al. 1991;Chen et al. 2007). Donors can be from the sister chromosome (allelic gene conversion) or dispersed sequences not at the same locus (ectopic gene conversion).Current genomic engineering methods use a DSB induced at a target genomic locus to generate disrupting mutations, driven by NHEJ, or to introduce new genetic sequences, driven by homology-directed repair (HDR). Several techniques have been developed to introduce target-specific DSBs, including zincfinger nucleases, transcription-activator-like effecter nucleases, and, most recently, clustered regularly-interspaced palindromic repeats (CRISPR) (Jinek et al. 2012;Doudna and Sontheimer 2014). Cas9 is the endonuclease of the type II CRISPR system and creates a DSB at genomic locations directed by a guide RNA (gRNA). The CRISPR/Cas9 system is favored for its high efficiency and ability to use a small gRNA to specifically target most genomic DNA locations (Cong et al. 2013;Hsu et a...

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