Conditional gene expression in invertebrate animal models

Brecht Driesschaert; Lucas Mergan; Liesbet Temmerman

doi:10.1016/j.jgg.2021.01.005

Volume 48 Issue 1

Jan. 2021

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Conditional gene expression in invertebrate animal models

doi: 10.1016/j.jgg.2021.01.005

Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59 - Box 2465, B-3000 Leuven, Belgium

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Corresponding author: E-mail address: Liesbet.Temmerman@kuleuven.be (Liesbet Temmerman)
Publish Date: 2021-01-20

Abstract

Abstract

A mechanistic understanding of biology requires appreciating spatiotemporal aspects of gene expression and its functional implications. Conditional expression allows for (ir)reversible switching of genes on or off, with the potential of spatial and/or temporal control. This provides a valuable complement to the more often used constitutive gene (in)activation through mutagenesis, providing tools to answer a wider array of research questions across biological disciplines. Spatial and/or temporal control are granted primarily by (combinations of) specific promoters, temperature regimens, compound addition, or illumination. The use of such genetic tool kits is particularly widespread in invertebrate animal models because they can be applied to study biological processes in short time frames and on large scales, using organisms amenable to easy genetic manipulation. Recent years witnessed an exciting expansion and optimization of such tools, of which we provide a comprehensive overview and discussion regarding their use in invertebrates. The mechanism, applicability, benefits, and drawbacks of each of the systems, as well as further developments to be expected in the foreseeable future, are highlighted.
- Conditional gene expression,
- Spatiotemporal control,
- Invertebrate,
- Model organism

These authors contributed equally to this work.

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References(198)

References

[1]	Afify, A., Betz, J.F., Riabinina, O., Lahondere, C., Potter, C.J., 2019. Commonly Used Insect Repellents Hide Human Odors from Anopheles Mosquitoes. Curr. Biol. 29, 3669-3680.
[2]	Ahringer, J., 2006. Reverse genetics, in: The C. elegans Research Community (Ed.), WormBook. WormBook.
[3]	Aoki, W., Matsukura, H., Yamauchi, Y., Yokoyama, H., Hasegawa, K., Shinya, R., Ueda, M., 2018. Cellomics approach for high-throughput functional annotation of Caenorhabditis elegans neural network. Sci. Rep. 8, 10380.
[4]	Araki, K., Araki, M., Yamamura, K.I., 1997. Targeted integration of DNA using mutant lox sites in embryonic stem cells. Nucleic Acids Res. 25, 868-872.
[5]	Armenti, S.T., Lohmer, L.L., Sherwood, D.R., Nance, J., 2014. Repurposing an endogenous degradation system for rapid and targeted depletion of C. elegans proteins. Development 141, 4640-4647.
[6]	Aubrey, B.J., Kelly, G.L., Kueh, A.J., Brennan, M.S., O’Connor, L., Milla, L., Wilcox, S., Tai, L., Strasser, A., Herold, M.J., 2015. An inducible lentiviral guide RNA platform enables the identification of tumor-essential genes and tumor-promoting mutations in vivo. Cell Rep.. 10, 1422-1432.
[7]	Bacaj, T., Shaham, S., 2007. Temporal Control of Cell-Specific Transgene Expression in Caenorhabditis elegans. Genetics 176, 2651-2655.
[8]	Bapst, A.M., Dahl, S.L., Knopfel, T., Wenger, R.H., 2020. Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription. Biochim. Biophys. Acta - Gene Regul. Mech. 1863, 194568.
[9]	Barwell, T., DeVeale, B., Poirier, L., Zheng, J., Seroude, F., Seroude, L., 2017. Regulating the UAS/GAL4 system in adult Drosophila with Tet-off GAL80 transgenes. PeerJ 5, e4167.
[10]	Batey, R.T., 2006. Structures of regulatory elements in mRNAs. Curr. Opin. Struct. Biol. 16, 299-306.
[11]	Baum, J.A., Geever, R., Giles, N.H., 1987. Expression of qa-1F activator protein: identification of upstream binding sites in the qa gene cluster and localization of the DNA-binding domain. Mol. Cell. Biol. 7, 1256-1266.
[12]	Bello, B., Resendez-perez, D., Gehring, W.J., 1998. Spatial and temporal targeting of gene expression in Drosophila by means of a tetracycline-dependent transactivator system. Development 125, 2193-2202.
[13]	Bieschke, E.T., Wheeler, J.C., Tower, J., 1998. Doxycycline-induced transgene expression during Drosophila development and aging. Mol. Gen. Genet. MGG 258, 571-579.
[14]	Boulina, M., Samarajeewa, H., Baker, J.D., Kim, M.D., Chiba, A., 2013. Live imaging of multicolor-labeled cells in Drosophila. Development 140, 1605-1613.
[15]	Brand, A.H., Perrimon, N., 1993. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118, 401-415.
[16]	Broach, J.R., Hicks, J.B., 1980. Replication and recombination functions associated with the yeast plasmid, 2μ circle. Cell 21, 501-508.
[17]	Brochta, D.A.O., Pilitt, K.L., Harrell, R.A., Aluvihare, C., Alford, R.T., 2012. Gal4-based Enhancer-Trapping in the Malaria Mosquito Anopheles stephensi. G3 - Genes\|Genomes\|Genetics 2, 1305-1315.
[18]	Bulgakov, V.P., Odintsova, N.A., Plotnikov, S. V, Kiselev, K. V, Zacharov, E. V, Zhuravlev, Y.N., 2002. Gal4-Gene-Dependent Alterations of Embryo Development and Cell Growth in Primary Culture of Sea Urchins. Mar. Biotechnol. 4, 480-486.
[19]	Cambridge, S.B., 1997. Drosophila Mitotic Domain Boundaries as Cell Fate Boundaries. Science 277, 825-828.
[20]	Caussinus, E., Kanca, O., Affolter, M., 2012. Fluorescent fusion protein knockout mediated by anti-GFP nanobody. Nat. Struct. Mol. Biol. 19, 117-121.
[21]	Chan, Y.-B., Alekseyenko, O. V., Kravitz, E.A., 2015. Optogenetic Control of Gene Expression in Drosophila. PLoS One 10, e0138181.
[22]	Chen, X., Liao, S., Huang, X., Xu, T., Feng, X., Guang, S., 2018. Targeted Chromosomal Rearrangements via Combinatorial Use of CRISPR/Cas9 and Cre/LoxP Technologies in Caenorhabditis elegans. G3 - Genes\|Genomes\|Genetics 8, 2697-2707.
[23]	Chen, X., Tan, A., Palli, S.R., 2020. Identification and functional analysis of promoters of heat-shock genes from the fall armyworm, Spodoptera frugiperda. Sci. Rep. 10, 2-10.
[24]	Cho, U., Zimmerman, S.M., Chen, L., Owen, E., Kim, J. V., Kim, S.K., Wandless, T.J., 2013. Rapid and Tunable Control of Protein Stability in Caenorhabditis elegans Using a Small Molecule. PLoS One 8, e72393.
[25]	Chylinski, K., Hubmann, M., Hanna, R.E., Yanchus, C., Michlits, G., Uijttewaal, E.C.H., Doench, J., Schramek, D., Elling, U., 2019. CRISPR-Switch regulates sgRNA activity by Cre recombination for sequential editing of two loci. Nat. Commun. 10, 5454.
[26]	Davis, K.M., Pattanayak, V., Thompson, D.B., Zuris, J.A., Liu, D.R., 2015. Small molecule-triggered Cas9 protein with improved genome-editing specificity. Nat. Chem. Biol. 11, 316-318.
[27]	Davis, L., Radman, I., Goutou, A., Tynan, A., Baxter, K., Xi, Z., Chin, J.W., Greiss, S., 2020. Optically splitting symmetric neuron pairs in C. elegans. Preprint on bioRxiv.
[28]	Davis, M.W., Morton, J.J., Carroll, D., Jorgensen, E.M., 2008. Gene Activation Using FLP Recombinase in C. elegans. PLoS Genet. 4.
[29]	del Valle Rodriguez, A., Didiano, D., Desplan, C., 2012. Power tools for gene expression and clonal analysis in Drosophila. Nat. Methods 9, 47-55.
[30]	Deng, W., Bates, J.A., Wei, H., Bartoschek, M.D., Conradt, B., Leonhardt, H., 2020. Tunable light and drug induced depletion of target proteins. Nat. Commun. 11, 304.
[31]	Didomenico, B.J., Bugaisky, G.E., Lindquist, S., 1982. The heat shock response is self-regulated at both the transcriptional and posttranscriptional levels. Cell 31, 593-603.
[32]	Dietzl, G., Chen, D., Schnorrer, F., Su, K.-C., Barinova, Y., Fellner, M., Gasser, B., Kinsey, K., Oppel, S., Scheiblauer, S., Couto, A., Marra, V., Keleman, K., Dickson, B.J., 2007. A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448, 151-156.
[33]	Dionne, H., Hibbard, K.L., Cavallaro, A., Kao, J., Rubin, G.M., 2018. Genetic Reagents for Making Split-GAL4 Lines in Drosophila. Genetics 209, 31-35.
[34]	Dolan, M.-J., Luan, H., Shropshire, W.C., Sutcliffe, B., Cocanougher, B., Scott, R.L., Frechter, S., Zlatic, M., Jefferis, G.S.X.E., White, B.H., 2017. Facilitating Neuron-Specific Genetic Manipulations in Drosophila melanogaster using a split Gal4 repressor. Genetics 206, 775-784.
[35]	Dow, L.E., Fisher, J., O’Rourke, K.P., Muley, A., Kastenhuber, E.R., Livshits, G., Tschaharganeh, D.F., Socci, N.D., Lowe, S.W., 2015. Inducible in vivo genome editing with CRISPR-Cas9. Nat. Biotechnol. 33, 390-394.
[36]	Duan, J., Xu, H., Ma, S., Guo, H., Wang, F., Zhao, P., Xia, Q., 2013. Cre-mediated targeted gene activation in the middle silk glands of transgenic silkworms (Bombyx mori). Transgenic Res. 22, 607-619.
[37]	Duffy, J.B., 2002. GAL4 System in Drosophila: A Fly Geneticist’s Swiss Army Knife. Genesis 34, 1-15.
[38]	Faden, F., Ramezani, T., Mielke, S., Almudi, I., Nairz, K., Froehlich, M.S., Hockendorff, J., Brandt, W., Hoehenwarter, W., Dohmen, R.J., Schnittger, A., Dissmeyer, N., 2016. Phenotypes on demand via switchable target protein degradation in multicellular organisms. Nat. Commun. 7, 12202.
[39]	Feil, R., Wagner, J., Metzger, D., Chambon, P., 1997. Regulation of Cre Recombinase Activity by Mutated Estrogen Receptor Ligand-Binding Domains. Biochem. Biophys. Res. Commun. 237, 752-757.
[40]	Felletti, M., Hartig, J.S., 2017. Ligand-dependent ribozymes. Wiley Interdiscip. Rev. RNA 8, e1395.
[41]	Fielmich, L.-E., Schmidt, R., Dickinson, D.J., Goldstein, B., Akhmanova, A., van den Heuvel, S., 2018. Optogenetic dissection of mitotic spindle positioning in vivo. Elife 7, e38198.
[42]	Fisher, Y.E., Yang, H.H., Isaacman-beck, J., Xie, M., Gohl, D.M., Clandinin, T.R., 2017. FlpStop, a tool for conditional gene control in Drosophila. Elife 6, 1-33.
[43]	Flavell, S.W., Pokala, N., Macosko, E.Z., Albrecht, D.R., Larsch, J., Bargmann, C.I., 2013. Serotonin and the Neuropeptide PDF Initiate and Extend Opposing Behavioral States in C. elegans. Cell 154, 1023-1035.
[44]	Ford, D., Hoe, N., Landis, G., Tozer, K., Luu, A., Bhole, D., Badrinath, A., Tower, J., 2007. Alteration of Drosophila life span using conditional, tissue-specific expression of transgenes triggered by doxycyline or RU486/Mifepristone. Exp. Gerontol. 42, 483-497.
[45]	Fortin, P.-Y., Genevois, C., Chapolard, M., Santalucia, T., Planas, A.M., Couillaud, F., 2014. Dual-reporter in vivo imaging of transient and inducible heat-shock promoter activation. Biomed. Opt. Express 5, 457.
[46]	Frickenhaus, M., Wagner, M., Mallik, M., Catinozzi, M., Storkebaum, E., 2015. Highly efficient cell-type-specific gene inactivation reveals a key function for the Drosophila FUS homolog cabeza in neurons. Sci. Rep. 5, 1-10.
[47]	Germani, F., Bergantinos, C., Johnston, L.A., 2018. Mosaic Analysis in Drosophila. Genetics 208, 473-490.
[48]	Ghosh, D., Seydoux, G., 2008. Inhibition of Transcription by the Caenorhabditis elegans Germline Protein PIE-1: Genetic Evidence for Distinct Mechanisms Targeting Initiation and Elongation. Genetics 178, 235-243.
[49]	Giles, N.H., Geever, R.F., Asch, D.K., Avalos, J., Case, M.E., 1991. Organization and Regulation of the Qa (Quinic Acid) Genes in Neurospora crassa and Other Fungi. J. Hered. 82, 1-7.
[50]	Gohl, D.M., Silies, M.A., Gao, X.J., Bhalerao, S., Luongo, F.J., Lin, C., Potter, C.J., Clandinin, T.R., 2011. A versatile in vivo system for directed dissection of gene expression patterns. Nat. Methods 8, 231-241.
[51]	Golic, K.G., Lindquist, S., 1989. The FLP Recombinase of Yeast Catalyzes Site-Specific Recombination in the Drosophila Genome. Cell 59, 499-509.
[52]	Gossen, M., Bujard, H., 1992. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. 89, 5547-5551.
[53]	Gossen, M., Freundlieb, S., Bender, G., Muller, G., Hillen, W., Bujard, H., 1995. Transcriptional activation by tetracyclines in mammalian cells. Science 268, 1766-1769.
[54]	Groth, A.C., 2004. Construction of Transgenic Drosophila by Using the Site-Specific Integrase From Phage C31. Genetics 166, 1775-1782.
[55]	Haghighat-Khah, R.E., Scaife, S., Martins, S., St John, O., Matzen, K.J., Morrison, N., Alphey, L., 2015. Site-Specific Cassette Exchange Systems in the Aedes aegypti Mosquito and the Plutella xylostella Moth. PLoS One 10, e0121097.
[56]	Halfon, M.S., Kose, H., Chiba, A., Keshishian, H., 1997. Targeted gene expression without a tissue-specific promoter: Creating mosaic embryos using laser-induced single-cell heat shock. Proc. Natl. Acad. Sci. 94, 6255-6260.
[57]	Hara, K., Kuwayama, H., Inukai, Y., 2009. A novel fusion protein that functions as an enhanced green fluorescent protein reporter and a tetracycline-controlled transcriptional activator. Dev. Genes Evol. 219, 103-110.
[58]	Hara, K., Kuwayama, H., Yaginuma, T., Niimi, T., 2008. Establishment of a Tetracycline-Off System using a piggyBac-based Vector as a Gene Functional Analysis Tool for the Temporal Targeting of Gene Expression. J. Insect Biotechnol. Sericology 77, 159-166.
[59]	Harmansa, S., Hamaratoglu, F., Affolter, M., Caussinus, E., 2015. Dpp spreading is required for medial but not for lateral wing disc growth. Nature 527, 317-322.
[60]	Hayashi, S., Ito, K., Sado, Y., Taniguchi, M., Akimoto, A., Takeuchi, H., Aigaki, T., Matsuzaki, F., Nakagoshi, H., Tanimura, T., Ueda, R., Uemura, T., Yoshihara, M., Goto, S., 2002. GETDB, a Database Compiling Expression Patterns and Molecular Locations of a Collection of Gal4 Enhancer Traps. Genesis 34, 58-61.
[61]	Heidmann, D., Lehner, C.F., 2001. Reduction of Cre recombinase toxicity in proliferating Drosophila cells by estrogen-dependent activity regulation. Dev. Genes Evol. 211, 458-465.
[62]	Heitzler, P., Simpson, P., 1991. The choice of cell fate in the epidermis of Drosophila. Cell 64, 1083-1092.
[63]	Hercus, M.J., Loeschcke, V., Rattan, S.I.S., 2003. Lifespan extension of Drosophila melanogaster through hormesis by repeated mild heat stress. Biogerontology 4, 149-156.
[64]	Hermann, A., Liewald, J.F., Gottschalk, A., 2015. A photosensitive degron enables acute light-induced protein degradation in the nervous system. Curr. Biol. 25, R749-R750.
[65]	Hill, A.J., Mansfield, R., Lopez, J.M.N.G., Raizen, D.M., Van Buskirk, C., 2014. Cellular Stress Induces a Protective Sleep-like State in C. elegans. Curr. Biol. 24, 2399-2405.
[66]	Hoier, E.F., Mohler, W.A., Kim, S.K., Hajnal, A., 2000. The Caenorhabditis elegans APC-related gene apr-1 is required for epithelial cell migration and Hox gene expression. Genes Dev. 14, 874-886.
[67]	Höorner, M., Muüller, K., Weber, W., 2017. Light-responsive promoters. In: Gould, D. (Ed.), Mammalian Synthetic Promoters. Humana, New York, pp. 173-186.
[68]	Hubbard, E.J.A., 2014. FLP/FRT and Cre/lox recombination technology in C. elegans. Methods 68, 417-424.
[69]	Huiet, L., Giles, N.H., 1986. The qa repressor gene of Neurospora crassa: wild-type and mutant nucleotide sequences. Proc. Natl. Acad. Sci. 83, 3381-3385.
[70]	Huynh, N., Zeng, J., Liu, W., King-Jones, K., 2018. A Drosophila CRISPR/Cas9 Toolkit for Conditionally Manipulating Gene Expression in the Prothoracic Gland as a Test Case for Polytene Tissues. G3 8, 3593-3605.
[71]	Imamura, M., Nakai, J., Inoue, S., Quan, G.X., Kanda, T., Tamura, T., 2003. Targeted Gene Expression Using the GAL4/UAS System in the Silkworm Bombyx mori. Genetics 165, 1329-1340.
[72]	Jain, P.K., Ramanan, V., Schepers, A.G., Dalvie, N.S., Panda, A., Fleming, H.E., Bhatia, S.N., 2016. Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors. Angew. Chemie Int. Ed. 55, 12440-12444.
[73]	Jenett, A., Rubin, G.M., Ngo, T.B., Shepherd, D., Murphy, C., Dionne, H., Pfeiffer, B.D., Cavallaro, A., Hall, D., Jeter, J., Iyer, N., Fetter, D., Hausenfluck, J.H., Peng, H., Trautman, E.T., Svirskas, R.R., Myers, E.W., Iwinski, Z.R., Aso, Y., Depasquale, G.M., Enos, A., Hulamm, P., Chun, S., Lam, B., Li, H., Laverty, T.R., Long, F., Qu, L., Murphy, S.D., Rokicki, K., Safford, T., Shaw, K., Simpson, J.H., Sowell, A., Tae, S., Yu, Y., Zugates, C.T., 2012. Resource A GAL4-Driver Line Resource for Drosophila Neurobiology. CellReports 2, 991-1001.
[74]	Jia, Y., Xu, R.-G., Ren, X., Ewen-Campen, B., Rajakumar, R., Zirin, J., Yang-Zhou, D., Zhu, R., Wang, F., Mao, D., Peng, P., Qiao, H.-H., Wang, X., Liu, L.-P., Xu, B., Ji, J.-Y., Liu, Q., Sun, J., Perrimon, N., Ni, J.-Q., 2018. Next-generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM. Proc. Natl. Acad. Sci. 115, 4719-4724.
[75]	Kaczmarczyk, S.J., 2001. A single vector containing modified cre recombinase and LOX recombination sequences for inducible tissue-specific amplification of gene expression. Nucleic Acids Res. 29, e56.
[76]	Kage-Nakadai, E., Imae, R., Suehiro, Y., Yoshina, S., Hori, S., Mitani, S., 2014. A Conditional Knockout Toolkit for Caenorhabditis elegans Based on the Cre/loxP Recombination. PLoS One 9, e114680.
[77]	Kakidani, H., Ptashne, M., 1988. GAL4 activates gene expression in mammalian cells. Cell 52, 161-167.
[78]	Kallunki, T., Barisic, M., Jaattela, M., Liu, B., 2019. How to Choose the Right Inducible Gene Expression System for Mammalian Studies? Cells 8, 796.
[79]	Karasaki, N., Mon, H., Takahashi, M., Lee, J.M., Koga, K., Kawaguchi, Y., Kusakabe, T., 2009. Establishment of tetracycline-inducible gene expression systems in the silkworm, Bombyx mori. Biotechnol. Lett. 31, 495-500.
[80]	Kawaguchi, A., Utsumi, N., Morita, M., Ohya, A., Wada, S., 2015. Application of the cis-regulatory region of a heat-shock protein 70 gene to heat-inducible gene expression in the ascidian Ciona intestinalis. Genesis 53, 170-182.
[81]	Kennerdell, J.R., Carthew, R.W., 2000. Heritable gene silencing in Drosophila using double-stranded RNA. Nat. Biotechnol. 18, 896-898.
[82]	Kerk, S.Y., Kratsios, P., Hart, M., Mourao, R., Hobert, O., 2017. Diversification of C. elegans Motor Neuron Identity via Selective Effector Gene Repression. Neuron 93, 80-98.
[83]	Kim, J.C., Cook, M.N., Carey, M.R., Shen, C., Regehr, W.G., Dymecki, S.M., 2009. Linking Genetically Defined Neurons to Behavior through a Broadly Applicable Silencing Allele. Neuron 63, 305-315.
[84]	Knapp, J.-M., Chung, P., Simpson, J.H., 2015. Generating Customized Transgene Landing Sites and Multi-Transgene Arrays in Drosophila Using phiC31 Integrase. Genetics 199, 919-934.
[85]	Kokoza, V.A., Raikhel, A.S., 2011. Targeted gene expression in the transgenic Aedes aegypti using the binary Gal4-UAS system. Insect Biochem. Mol. Biol. 41, 637-644.
[86]	Konermann, S., Brigham, M.D., Trevino, A.E., Hsu, P.D., Heidenreich, M., Le Cong, Platt, R.J., Scott, D.A., Church, G.M., Zhang, F., 2013. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500, 472-476.
[87]	Kuhlman, S.J., Huang, Z.J., 2008. High-Resolution Labeling and Functional Manipulation of Specific Neuron Types in Mouse Brain by Cre-Activated Viral Gene Expression. PLoS One 3, e2005.
[88]	Labbe, G.M.C., Nimmo, D.D., Alphey, L., 2010. piggybac- and PhiC31-Mediated Genetic Transformation of the Asian Tiger Mosquito, Aedes albopictus (Skuse). PLoS Negl. Trop. Dis. 4, e788.
[89]	Lai, S.L., Lee, T., 2006. Genetic mosaic with dual binary transcriptional systems in Drosophila. Nat. Neurosci. 9, 703-709.
[90]	Lewandoski, M., 2001. Conditional control of gene expression in the mouse. Nat. Rev. Genet. 2, 743-755.
[91]	Lin, C.-C., Potter, C.J., 2016. Editing Transgenic DNA Components by Inducible Gene Replacement in Drosophila melanogaster. Genetics 203, 1613-1628.
[92]	Lin, J.Y., Sann, S.B., Zhou, K., Nabavi, S., Proulx, C.D., Malinow, R., Jin, Y., Tsien, R.Y., 2013. Optogenetic Inhibition of Synaptic Release with Chromophore-Assisted Light Inactivation (CALI). Neuron 79, 241-253.
[93]	Lin, S., Ewen-Campen, B., Ni, X., Housden, B.E., Perrimon, N., 2015. In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila. Genetics 201, 433-442.
[94]	Lis, J.T., Simon, J.A., Sutton, C.A., 1983. New heat shock puffs and β-galactosidase activity resulting from transformation of Drosophila with an hsp70-lacZ hybrid gene. Cell 35, 403-410.
[95]	Lithgow, G.J., White, T.M., Hinerfeld, D.A., Johnson, T.E., 1994. Thermotolerance of a Long-lived Mutant of Caenorhabditis elegans. J. Gerontol. 49, B270-B276.
[96]	Liu, P., Long, L., Xiong, K., Yu, B., Chang, N., Xiong, J.-W., Zhu, Z., Liu, D., 2014. Heritable/conditional genome editing in C. elegans using a CRISPR-Cas9 feeding system. Cell Res. 24, 886-889.
[97]	Lo, T., Pickle, C.S., Lin, S., Ralston, E.J., Gurling, M., Schartner, C.M., Bian, Q., Doudna, J.A., Meyer, B.J., 2013. Precise and Heritable Genome Editing in Evolutionarily Diverse Nematodes Using TALENs and CRISPR/Cas9 to Engineer Insertions and Deletions. Genetics 195, 331-348.
[98]	Long, D., Zhao, A., Chen, X., Zhang, Y., Lu, W., Guo, Q., Handler, A.M., Xiang, Z., 2012. FLP Recombinase-Mediated Site-Specific Recombination in Silkworm, Bombyx mori. PLoS One 7, e40150.
[99]	Luan, H., Peabody, N.C., Vinson, C.R., White, B.H., 2006. Refined Spatial Manipulation of Neurotechnique Neuronal Function by Combinatorial Restriction of Transgene Expression. Neuron 52, 425-436.
[100]	Luo, J., Shen, P., Chen, J., 2019. A modular toolset of phiC31-based fluorescent protein tagging vectors for Drosophila. Fly (Austin). 13, 29-41.
[101]	Lycett, G.J., Kafatos, F.C., Loukeris, T.G., 2004. Conditional Expression in the Malaria Mosquito Anopheles stephensi With Tet-On and Tet-Off Systems. Genetics 167, 1781-1790.
[102]	Lynd, A., Lycett, G.J., 2012. Development of the Bi-Partite Gal4-UAS System in the African Malaria Mosquito, Anopheles gambiae. PLoS One 7.
[103]	Macosko, E.Z., Pokala, N., Feinberg, E.H., Chalasani, S.H., Butcher, R.A., Clardy, J., Bargmann, C.I., 2009. A hub-and-spoke circuit drives pheromone attraction and social behaviour in C . elegans. Nature 458, 1171-1176.
[104]	Maltzman, J.S., Turka, L.A., 2007. Conditional Gene Expression: A New Tool for the Transplantologist. Am. J. Transplant. 7, 733-740.
[105]	Manivannan, S.N., Pandey, P., Nagarkar-jaiswal, S., 2019. Flip-flop Mediated Conditional Gene Inactivation in Drosophila. Bio-protocol 9, 1-17.
[106]	Mann, K., Gordon, M.D., Scott, K., 2013. A pair of interneurons influences the choice between feeding and locomotion in Drosophila. Neuron 79, 754-765.
[107]	Mao, C., Wikramanayake, A.H., Gan, L., Chuang, C., Summers, R.G., Klein, W.H., 1996. Altering cell fates in sea urchin embryos by overexpressing SpOtx, an orthodenticle-related protein. Development 122, 1489-1498.
[108]	Mao, S., Qi, Y., Zhu, H., Huang, X., Zou, Y., Chi, T., 2019. A Tet/Q Hybrid System for Robust and Versatile Control of Transgene Expression in C. elegans. iScience 11, 224-237.
[109]	Matthews, B.J., Younger, M.A., Vosshall, L.B., 2019. The ion channel ppk301 controls freshwater egg-laying in the mosquito Aedes aegypti. Elife 8, e43963.
[110]	McGuire, S.E., Le, P.T., Osborn, A.J., Matsumoto, K., Davis, R.L., 2003. Spatiotemporal Rescue of Memory Dysfunction in Drosophila. Science 302, 1765-1768.
[111]	McLeod, M., Craft, S., Broach, J.R., 1986. Identification of the crossover site during FLP-mediated recombination in the Saccharomyces cerevisiae plasmid 2 microns circle. Mol. Cell. Biol. 6, 3357-3367.
[112]	McMahon, A.P., Novak, T.J., Britten, R.J., Davidson, E.H., 1984. Inducible expression of a cloned heat shock fusion gene in sea urchin embryos. Proc. Natl. Acad. Sci. U. S. A. 81, 7490-7494.
[113]	Meredith, J.M., Basu, S., Nimmo, D.D., Larget-Thiery, I., Warr, E.L., Underhill, A., McArthur, C.C., Carter, V., Hurd, H., Bourgouin, C., Eggleston, P., 2011. Site-Specific Integration and Expression of an Anti-Malarial Gene in Transgenic Anopheles gambiae Significantly Reduces Plasmodium Infections. PLoS One 6, e14587.
[114]	Mondal, K., Dastidar, A.G., Singh, G., Madhusudhanan, S., Gande, S.L., VijayRaghavan, K., Varadarajan, R., 2007. Design and Isolation of Temperature-sensitive Mutants of Gal4 in Yeast and Drosophila. J. Mol. Biol. 370, 939-950.
[115]	Monsalve, G.C., Yamamoto, K.R., Ward, J.D., 2019. A New Tool for Inducible Gene Expression in Caenorhabditis elegans. Genetics 211, 419-430.
[116]	Morris, A.C., Schaub, T.L., James, A.A., 1991. FLP-mediated recombination in the vector mosquite, Aedes aegypti. Nucleic Acids Res. 19, 5895-5900.
[117]	Muller, K., Engesser, R., Schulz, S., Steinberg, T., Tomakidi, P., Weber, C.C., Ulm, R., Timmer, J., Zurbriggen, M.D., Weber, W., 2013. Multi-chromatic control of mammalian gene expression and signaling. Nucleic Acids Res. 41, e124-e124.
[118]	Muller, K., Zurbriggen, M.D., Weber, W., 2014. Control of gene expression using a red- and far-red light-responsive bi-stable toggle switch. Nat. Protoc. 9, 622-632.
[119]	Munoz-jimenez, C., Ayuso, C., Dobrzynska, A., Torres-Mendez, A., Ruiz, P. de la C., Askjaer, P., 2017. An Efficient FLP-Based Toolkit for Spatiotemporal Control of Gene Expression in Caenorhabditis elegans. Genetics 206, 1763-1778.
[120]	Nance, J., Froekjaer-Jensen, C., 2019. The Caenorhabditis elegans Transgenic Toolbox. Genetics 212, 959-990.
[121]	Nern, A., Pfeiffer, B.D., Svoboda, K., Rubin, G.M., 2011. Multiple new site-specific recombinases for use in manipulating animal genomes. Proc. Natl. Acad. Sci. 108, 14198-14203.
[122]	Newsome, T.P., Asling, B., Dickson, B.J., 2000. Analysis of Drosophila photoreceptor axon guidance in eye-specific mosaics. Development 127, 851-860.
[123]	Ni, J.-Q., Zhou, R., Czech, B., Liu, L.-P., Holderbaum, L., Yang-Zhou, D., Shim, H.-S., Tao, R., Handler, D., Karpowicz, P., Binari, R., Booker, M., Brennecke, J., Perkins, L.A., Hannon, G.J., Perrimon, N., 2011. A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat. Methods 8, 405-407.
[124]	Nihongaki, Y., Yamamoto, S., Kawano, F., Suzuki, H., Sato, M., 2015. CRISPR-Cas9-based Photoactivatable Transcription System. Chem. Biol. 22, 169-174.
[125]	Nikitina, E.A., Kaminskaya, A.N., Molotkov, D.A., Popov, A. V, Savvateeva-Popova, E. V, 2014. Effect of heat shock on courtship behavior, sound production, and learning in comparison with the brain content of LIMK1 in Drosophila melanogaster males with altered structure of the limk1 gene. J. Evol. Biochem. Physiol. 50, 154-166.
[126]	Nimmo, D.D., Alphey, L., Meredith, J.M., Eggleston, P., 2006. High efficiency site-specific genetic engineering of the mosquito genome. Insect Mol. Biol. 15, 129-136.
[127]	Nonet, M.L., 2020. Efficient Transgenesis in Caenorhabditis elegans Using Flp Recombinase-Mediated Cassette Exchange. Genetics 215, 903-921.
[128]	Osterwalder, T., Yoon, K.S., White, B.H., Keshishian, H., 2001. A conditional tissue-specific transgene expression system using inducible GAL4. Proc. Natl. Acad. Sci. 98, 12596-12601.
[129]	Pani, A.M., Goldstein, B., 2018. Direct visualization of a native Wnt in vivo reveals that a long-range Wnt gradient forms by extracellular dispersal. Elife 7, e38325.
[130]	Patel, T., Hobert, O., 2017. Coordinated control of terminal differentiation and restriction of cellular plasticity. Elife 6, e24100.
[131]	Patel, V.B., Schweizer, M., Dykstra, C.C., Kushner, S.R., Giles, N.H., 1981. Genetic organization and transcriptional regulation in the qa gene cluster of Neurospora crassa. Proc. Natl. Acad. Sci. 78, 5783-5787.
[132]	Perez-Garijo, A., Fuchs, Y., Steller, H., 2013. Apoptotic cells can induce non-autonomous apoptosis through the TNF pathway. Elife 2013, e01004.
[133]	Pfeiffer, B.D., Ngo, T.B., Hibbard, K.L., Murphy, C., Jenett, A., Truman, J.W., Rubin, G.M., 2010. Refinement of Tools for Targeted Gene Expression in Drosophila. Genetics 186, 735-755.
[134]	Poirier, L., Shane, A., Zheng, J., Seroude, L., 2008. Characterization of the Drosophila Gene-Switch system in aging studies: a cautionary tale. Aging Cell 7, 758-770.
[135]	Polstein, L.R., Gersbach, C.A., 2015. A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat. Chem. Biol. 11, 198-200.
[136]	Polstein, L.R., Gersbach, C.A., 2012. Light-Inducible Spatiotemporal Control of Gene Activation by Customizable Zinc Finger Transcription Factors. J. Am. Chem. Soc. 134, 16480-16483.
[137]	Port, F., Bullock, S.L., 2016. Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs. Nat. Methods 13, 852-854.
[138]	Port, F., Starostecka, M., Boutros, M., 2020a. Multiplexed conditional genome editing with Cas12a in Drosophila. Proc. Natl. Acad. Sci. 117, 22890-22899.
[139]	Port, F., Strein, C., Stricker, M., Rauscher, B., Heigwer, F., Zhou, J., Beyersdorffer, C., Frei, J., Hess, A., Kern, K., Lange, L., Langner, N., Malamud, R., Pavlovic, B., Radecke, K., Schmitt, L., Voos, L., Valentini, E., Boutros, M., 2020b. A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila. Elife 9, e53865.
[140]	Potter, C.J., Luo, L., 2011. Using the Q system in Drosophila melanogaster. Nat. Protoc. 6, 1105-1120.
[141]	Potter, C.J., Tasic, B., Russler, E. V., Liang, L., Luo, L., 2010. The Q System: A Repressible Binary System for Transgene Expression, Lineage Tracing, and Mosaic Analysis. Cell 141, 536-548.
[142]	Riabinina, O., Luginbuhl, D., Marr, E., Liu, S., Wu, M.N., Luo, L., Potter, C.J., 2015. Improved and expanded Q-system reagents for genetic manipulations. Nat. Methods 12, 219-222.
[143]	10.1007/978-1-4939-6371-3_3
[144]	Riabinina, O., Task, D., Marr, E., Lin, C.-C., Alford, R., O’Brochta, D.A., Potter, C.J., 2016. Organization of olfactory centres in the malaria mosquito Anopheles gambiae. Nat. Commun. 7, 13010.
[145]	Riabinina, O., Vernon, S.W., Dickson, B.J., Baines, R.A., 2019. Split-QF System for Fine-Tuned Transgene Expression in Drosophila. Genetics 212, 53-63.
[146]	Ritossa, F., 1962. A new puffing pattern induced by temperature shock and DNP in Drosophila. Experientia 18, 571-573.
[147]	Roman, G., Endo, K., Zong, L., Davis, R.L., 2001. P{Switch}, a system for spatial and temporal control of gene expression in Drosophila melanogaster. Proc. Natl. Acad. Sci. 98, 12602-12607.
[148]	Sauer, B., 1987. Functional Expression of the cre-lox Site-Specific Recombination System in the Yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 7, 2087-2096.
[149]	Sauer, B., Henderson, N., 1988. Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1. PNAS 85, 5166-5170.
[150]	Schetelig, M.F., Handler, A.M., 2013. A Functional Comparison of the 3xP3 Promoter by Recombinase-Mediated Cassette Exchange in Drosophila and a Tephritid Fly , Anastrepha suspensa. G3 - Genes\|Genomes\|Genetics 3, 687-693.
[151]	Schinko, J.B., Weber, M., Viktorinova, I., Kiupakis, A., Averof, M., Klingler, M., Wimmer, E.A., Bucher, G., 2010. Functionality of the GAL4/UAS system in Tribolium requires the use of endogenous core promoters. BMC Dev. Biol. 10, 53.
[152]	Schmidt-Supprian, M., Rajewsky, K., 2007. Vagaries of conditional gene targeting. Nat. Immunol. 8, 665-668.
[153]	Schnutgen, F., Doerflinger, N., Calleja, C., Wendling, O., Chambon, P., Ghyselinck, N.B., 2003. A directional strategy for monitoring Cre-mediated recombination at the cellular level in the mouse. Nat. Biotechnol. 21, 562-565.
[154]	Scialo, F., Sriram, A., Stefanatos, R., Sanz, A., 2016. Practical Recommendations for the Use of the GeneSwitch Gal4 System to Knock-Down Genes in Drosophila melanogaster. PLoS One 11, e0161817.
[155]	Sethi, S., Wang, J.W., 2017. A versatile genetic tool for post-translational control of gene expression in Drosophila melanogaster. Elife 6, e30327.
[156]	Shen, Z., Zhang, X., Chai, Y., Zhu, Z., Yi, P., Feng, G., Li, W., Ou, G., 2014. Conditional Knockouts Generated by Engineered CRISPR-Cas9 Endonuclease Reveal the Roles of Coronin in C. elegans Neural Development. Dev. Cell 30, 625-636.
[157]	Shimizu-Sato, S., Huq, E., Tepperman, J.M., Quail, P.H., 2002. A light-switchable gene promoter system. Nat. Biotechnol. 20, 1041-1044.
[158]	Siegal, M.L., Hartl, D.L., 1996. Transgene Coplacement and High Efficiency Site-Specific Recombination with the Cre/loxP System in Drosophila. Genetics 144, 715-726.
[159]	Silies, M., Gohl, D.M., Fisher, Y.E., Freifeld, L., Clark, D.A., Clandinin, T.R., 2013. Modular Use of Peripheral Input Channels Tunes Motion-Detecting Circuitry. Neuron 79, 111-127.
[160]	Silver, K., Jiang, H., Fu, J., Phillips, T.W., Beeman, R.W., Park, Y., 2015. The Tribolium castaneum cell line TcA: a new tool kit for cell biology. Sci. Rep. 4, 6840.
[161]	Stebbins, M.J., Urlinger, S., Byrne, G., Bello, B., Hillen, W., Yin, J.C.P., 2001. Tetracycline-inducible systems for Drosophila. Proc. Natl. Acad. Sci. 98, 10775-10780.
[162]	Stebbins, M.J., Yin, J.C.., 2001. Adaptable doxycycline-regulated gene expression systems for Drosophila. Gene 270, 103-111.
[163]	Steller, H., Pirrotta, V., 1985. Expression of the Drosophila white gene under the control of the hsp70 heat shock promoter. EMBO J. 4, 3765-3772.
[164]	Sternberg, N., 1981. Bacteriophage P1 site-specific recombination. J. Mol. Biol. 150, 603-608.
[165]	Stringham, E.G., Candido, E.P.M., 1993. Targeted single-cell induction of gene products in Caenorhabditis elegans: A new tool for developmental studies. J. Exp. Zool. 266, 227-233.
[166]	Stringham, E.G., Dixon, D.K., Jones, D., Candido, E.P.M., 1992. Temporal and spatial expression patterns of the small heat shock (hsp16) genes in transgenic Caenorhabditis elegans. Mol. Biol. Cell 3, 221-233.
[167]	Struhl, G., Basler, K., 1993. Organizing activity of wingless protein in Drosophila. Cell 72, 527-540.
[168]	Suster, M.L., Seugnet, L., Bate, M., Sokolowski, M.B., 2004. Refining GAL4-driven transgene expression in Drosophila with a GAL80 enhancer-trap. Genesis 39, 240-245.
[169]	Sweeney, S.T., Broadie, K., Keane, J., Niemann, H., O’Kane, C.J., 1995. Targeted expression of tetanus toxin light chain in Drosophila specifically eliminates synaptic transmission and causes behavioral defects. Neuron 14, 341-351.
[170]	Szuts, D., Bienz, M., 2000. LexA chimeras reveal the function of Drosophila Fos as a context-dependent transcriptional activator. Proc. Natl. Acad. Sci. 97, 5351-5356.
[171]	Tang, W., Hu, J.H., Liu, D.R., 2017. Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation. Nat. Commun. 8, 15939.
[172]	Tatsuke, T., Lee, J.M., 2013. Tightly controlled tetracycline-inducible transcription system for explosive gene expression in cultured silkworm cells. Arch. Insect Biochem. Physiol. 82, 173-182.
[173]	Ting, C.Y., Gu, S., Guttikonda, S., Lin, T.Y., White, B.H., Lee, C.H., 2011. Focusing transgene expression in Drosophila by Coupling Gal4 with a Novel Split-Lex A Expression System. Genetics 188, 229-233.
[174]	Tirian, L., Dickson, B.J., 2017. The VT GAL4, LexA, and split-GAL4 driver line collections for targeted expression in the Drosophila nervous system. Preprint on bioRxiv.
[175]	Trauth, J., Scheffer, J., Hasenjager, S., Taxis, C., 2019. Synthetic Control of Protein Degradation during Cell Proliferation and Developmental Processes. ACS Omega 4, 2766-2778.
[176]	Trost, M., Blattner, A.C., Lehner, C.F., 2016. Regulated protein depletion by the auxin-inducible degradation system in Drosophila melanogaster. Fly (Austin). 10, 35-46.
[177]	Urlinger, S., Baron, U., Thellmann, M., Hasan, M.T., Bujard, H., Hillen, W., 2000. Exploring the sequence space for tetracycline-dependent transcriptional activators: Novel mutations yield expanded range and sensitivity. Proc. Natl. Acad. Sci. 97, 7963-7968.
[178]	Vazquez-manrique, R.P., Legg, J.C., Olofsson, B., Ly, S., Baylis, H.A., 2010. Genomics Improved gene targeting in C. elegans using counter-selection and Flp-mediated marker excision. Genomics 95, 37-46.
[179]	Voutev, R., Hubbard, E.J.A., 2008. A ‘“FLP-Out”’ System for Controlled Gene Expression in Caenorhabditis elegans. Genetics 119, 103-119.
[180]	Wang, H., Liu, J., Gharib, S., Chai, C.M., Erich, M., Pokala, N., Sternberg, P.W., 2017. cGAL, a Temperature-Robust GAL4-UAS System for C. elegans. Nat. Methods 14, 145-148.
[181]	Wang, H., Liu, J., Yuet, K.P., Hill, A.J., Sternberg, P.W., 2018. Split cGAL, an intersectional strategy using a split intein for refined spatiotemporal transgene control in Caenorhabditis elegans. PNAS 115, 3900-3905.
[182]	Wang, S., Tang, N.H., Lara-Gonzalez, P., Zhao, Z., Cheerambathur, D.K., Prevo, B., Chisholm, A.D., Desai, A., Oegema, K., 2017. A toolkit for GFP-mediated tissue-specific protein degradation in C. elegans. Development 144, 2694-2701.
[183]	Wang, S.-R., Wu, L.-Y., Huang, H.-Y., Xiong, W., Liu, J., Wei, L., Yin, P., Tian, T., Zhou, X., 2020. Conditional control of RNA-guided nucleic acid cleavage and gene editing. Nat. Commun. 11, 91.
[184]	Wang, X., Chen, X., Yang, Y., 2012. Spatiotemporal control of gene expression by a light-switchable transgene system. Nat. Methods 9, 266-269.
[185]	Webster, N., Jin, J.R., Green, S., Hollis, M., Chambon, P., 1988. The yeast UASG is a transcriptional enhancer in human hela cells in the presence of the GAL4 trans-activator. Cell 52, 169-178.
[186]	Wei, X., Potter, C.J., Luo, L., Shen, K., 2012. Controlling gene expression with the Q repressible binary expression system in Caenorhabditis elegans. Nat. Methods 9, 391-395.
[187]	Weinberg, B.H., Cho, J.H., Agarwal, Y., Pham, N.T.H., Caraballo, L.D., Walkosz, M., Ortega, C., Trexler, M., Tague, N., Law, B., Benman, W.K.J., Letendre, J., Beal, J., Wong, W.W., 2019. High-performance chemical- and light-inducible recombinases in mammalian cells and mice. Nat. Commun. 10, 4845.
[188]	White, B.H., Osterwalder, T.P., Yoon, K.S., Joiner, W.J., Whim, M.D., Kaczmarek, L.K., Keshishian, H., Haven, N., 2001. Targeted Attenuation of Electrical Activity in Drosophila Using a Genetically Modified K+ Channel. Neuron 31, 699-711.
[189]	Wu, Q., Ploegh, H.L., Truttmann, M.C., 2017. Hepta-Mutant Staphylococcus aureus Sortase A (SrtA7m) as a Tool for in Vivo Protein Labeling in Caenorhabditis elegans. ACS Chem. Biol. 12, 664-673.
[190]	Wurmthaler, L.A., Sack, M., Gense, K., Hartig, J.S., Gamerdinger, M., 2019. A tetracycline-dependent ribozyme switch allows conditional induction of gene expression in Caenorhabditis elegans. Nat. Commun. 10, 491.
[191]	Xu, R.-G., Wang, X., Shen, D., Sun, J., Qiao, H.-H., Wang, F., Liu, L.-P., Ni, J.-Q., 2019. Perspectives on gene expression regulation techniques in Drosophila. J. Genet. Genomics 46, 213-220.
[192]	Xu, T., Rubin, G.M., 1993. Analysis of genetic mosaics in developing and adult Drosophila tissues. Development 117, 1223-1237.
[193]	Yamada, M., Suzuki, Y., Nagasaki, S.C., Okuno, H., Imayoshi, I., 2018. Light Control of the Tet Gene Expression System in Mammalian Cells. Cell Rep. 25, 487-500.
[194]	Yonemura, N., Tamura, T., Uchino, K., Kobayashi, I., Tatematsu, K., Iizuka, T., Tsubota, T., Sezutsu, H., Muthulakshmi, M., Nagaraju, J., Kusakabe, T., 2013. phiC31-integrase-mediated, site-specific integration of transgenes in the silkworm, Bombyx mori (Lepidoptera: Bombycidae). Appl. Entomol. Zool. 48, 265-273.
[195]	Zetsche, B., Volz, S.E., Zhang, F., 2015. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat. Biotechnol. 33, 139-142.
[196]	Zhang, L., Ward, J.D., Cheng, Z.Z., Dernburg, A.F., 2015. The auxin-inducible degradation (AID) system enables versatile conditional protein depletion in C. elegans. Development 142, 4374-4384.
[197]	Zhou, Q., Neal, S.J., Pignoni, F., 2016. Mutant analysis by rescue gene excision: New tools for mosaic studies in Drosophila. Genesis 54, 589-592.
[198]	Zhou, L., Schnitzler, A., Agapite, J., Schwartz, L.M., Steller, H., Nambu, J.R., 1997. Cooperative functions of the reaper and head involution defective genes in the programmed cell death of Drosophila central nervous system midline cells. Proc. Natl. Acad. Sci. 94, 5131-5136.