Resources
Below are some potentially useful resources for those looking to develop functional approaches in post-embryonic stages, or other contexts in which alternatives to intracellular injection are needed.
If you know of other resources that could be helpful to post here, please email us to let us know!
Below are some potentially useful resources for those looking to develop functional approaches in post-embryonic stages, or other contexts in which alternatives to intracellular injection are needed.
If you know of other resources that could be helpful to post here, please email us to let us know!
Delivery mechanisms
Some common approaches to deliver reagents into organisms and their cells include:
Molecular manipulations
Some common approaches to manipulate gene function include:
References
Some potentially useful references are below. (Have suggestions for other good references to post here? Please email to let us know!)
Adams, S., Pathak, P., Shao, H., Lok, J.B., and Pires-dasilva, A. (2019). Liposome-based transfection enhances RNAi and CRISPR- mediated mutagenesis in non- model nematode systems. Sci. Rep., 1–12.
Bannister, S., Antonova, O., Polo, A., Lohs, C., Hallay, N., Valinciute, A., Raible, F., and Tessmar-Raible, K. (2014). TALENs mediate efficient and heritable mutation of endogenous genes in the marine annelid Platynereis dumerilii. Genetics 197, 77–89.
Bezares-Calderon, L.A., Berger, J., Jasek, S., Veraszto, C., Mendes, S., Guhmann, M., Almeda, R., Shahidi, R., and Jekely, G. (2018). Neural circuitry of a polycystin-mediated hydrodynamic startle response for predator avoidance. Elife 7, 1–28.
Blum, M., De Robertis, E.M., Wallingford, J.B., and Niehrs, C. (2015). Morpholinos: Antisense and Sensibility. Dev. Cell 35, 145–149.
Chen, S., Lee, B., Lee, A.Y.F., Modzelewski, A.J., and He, L. (2016). Highly efficient mouse genome editing by CRISPR ribonucleoprotein electroporation of zygotes. J. Biol. Chem. 291, 14457–14467.
Conzelmann, M., Williams, E.A., Tunaru, S., Randel, N., Shahidi, R., Asadulina, A., Berger, J., Offermanns, S., and Jekely, G. (2013). Conserved MIP receptor-ligand pair regulates Platynereis larval settlement. Proc Natl Acad Sci U S A 110, 8224–8229.
Cwetsch, A.W., Pinto, B., Savardi, A., and Cancedda, L. (2018). Progress in Neurobiology In vivo methods for acute modulation of gene expression in the central nervous system. Prog. Neurobiol. 168, 69–85.
Demilly, A., Steinmetz, P., Gazave, E., Marchand, L., and Vervoort, M. (2013). Involvement of the Wnt/B-catenin pathway in neurectoderm architecture in Platynereis dumerilii. Nat. Commun. 4, 1911–1915.
Falk, J., Drinjakovic, J., Leung, K.M., Dwivedy, A., Regan, A.G., Piper, M., and Holt, C.E. (2007). Electroporation of cDNA / Morpholinos to targeted areas of embryonic CNS in Xenopus. 16, 1–16.
Fei, J., Knapp, D., Schuez, M., Murawala, P., Zou, Y., Singh, S.P., Drechsel, D., and Tanaka, E.M. (2016). Tissue- and time-directed electroporation of CAS9 protein – gRNA complexes in vivo yields ef fi cient multigene knockout for studying gene function in regeneration. 1–9.
Finn, J.D., Smith, A.R., Patel, M.C., Strapps, W.R., Chang, Y., Morrissey, D. V, Finn, J.D., Smith, A.R., Patel, M.C., Shaw, L., Youniss, M.R., Heteren, J. Van, Dirstine, T., Ciullo, C., Lescarbeau, R., Seitzer, J., Shah, R.R., Shah, A., Ling, D., Growe, J., Pink, M., Rohde, E., Wood, K. M.,
Salomon, W. E., Harrington, W. F., Dombrowski, C., Strapps, W. R., Chang, Y., and Morrissey, D. V. (2018). Report A Single Administration of CRISPR / Cas9 Lipid Nanoparticles Achieves Robust and Persistent In Vivo Genome Editing Report A Single Administration of CRISPR / Cas9 Lipid Nanoparticles Achieves Robust and Persistent In Vivo Genome Editing. CellReports 22, 2227–2235.
Flowers, G.P., Timberlake, A.T., Mclean, K.C., Monaghan, J.R., and Crews, C.M. (2014). Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease. 2165–2171.
Gandhi, S., Piacentino, M.L., Vieceli, F.M., and Bronner, M.E. (2017). Optimization of CRISPR/Cas9 genome editing for loss-of-function in the early chick embryo. Dev. Biol. 432, 86–97.
Genikhovich, G., Fried, P., Iber, D., and Technau, U. (2015). Axis Patterning by BMPs : Cnidarian Network Reveals Report Axis Patterning by BMPs : Cnidarian Network Reveals Evolutionary Constraints. Cell Rep., 1646–1654.
González-Estévez, C., Momose, T., Gehring, W.J., and Saló, E. (2003). Transgenic planarian lines obtained by electroporation using transposon-derived vectors and an eye-specific GFP marker. Proc. Natl. Acad. Sci. U. S. A. 100, 14046–14051.
Grillo, M., Konstantinides, N., and Averof, M. (2016). Old questions, new models: Unraveling complex organ regeneration with new experimental approaches. Curr. Opin. Genet. Dev. 40, 23–31.
Hajj, K.A., and Whitehead, K.A. (2017). Tools for translation: Non-viral materials for therapeutic mRNA delivery. Nat. Rev. Mater. 2, 1–17.
Hashimoto, M., and Takemoto, T. (2015). Electroporation enables the efficient mRNA delivery into the mouse zygotes and facilitates CRISPR/Cas9-based genome editing. Sci. Rep. 5, 1–3.
He, Z.Y., Men, K., Qin, Z., Yang, Y., Xu, T., and Wei, Y.Q. (2017). Non-viral and viral delivery systems for CRISPR-Cas9 technology in the biomedical field. Sci. China Life Sci. 60, 458–467.
Ikmi, A., Mckinney, S.A., Delventhal, K.M., and Gibson, M.C. (2014). TALEN and CRISPR/Cas9-mediated genome editing in the early-branching metazoan Nematostella vectensis. Nat. Commun. 5, 1–8.
Kanasty, R., Dorkin, J.R., Vegas, A., and Anderson, D. (2013). Delivery materials for siRNA therapeutics. Nat. Mater. 12, 967–977.
Kaneko, T., Sakuma, T., Yamamoto, T., and Mashimo, T. (2014). Simple knockout by electroporation of engineered endonucleases into intact rat embryos. Sci. Rep. 4, 1–5.
Karabulut, A., He, S., Chen, C., Mckinney, S.A., Matthew, C., and Gibson, M.C. (2018). Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone , Nematostella vectensis.
Klann, M., and Seaver, E.C. (2018). Functional role of pax6 in eye and central nervous system development in the annelid Capitella teleta. bioRxiv doi.org/10.1101/481135.
Lanza, A.R., and Seaver, E.C. (2018). An organizing role for the TGF-β signaling pathway in axes formation of the annelid Capitella teleta. Dev. Biol. 435, 26–40.
Lee, K., Conboy, M., Park, H.M., Jiang, F., Kim, H.J., Dewitt, M.A., Mackley, V.A., Chang, K., Rao, A., Skinner, C., Shobha, T., Mehdipour, M., Liu, H., Huang, W.C., Lan, F., Bray, N.L., Li, S., Corn, J.E., Kataoka, K., Doudna, J. A., Conboy, I., and Murthy, N. (2017). Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair. Nat. Biomed. Eng. 1, 889–901.
Liu, W., Wang, Y., Sun, Y., Wang, Y., Wang, Y., Chen, S., and Zhu, Z. (2005). Efficient RNA interference in zebrafish embryos using siRNA synthesized with SP6 RNA polymerase. 323–331.
Meyer, N.P., Boyle, M.J., Martindale, M.Q., and Seaver, E.C. (2010). A comprehensive fate map by intracellular injection of identified blastomeres in the marine polychaete Capitella teleta. Evodevo 1, 8.
Miura, H., Quadros, R.M., Gurumurthy, C.B., and Ohtsuka, M. (2018). Easi-CRISPR for creating knock-in and conditional knockout mouse models using long ssDNA donors. Nat. Protoc. 13, 195–215.
Moreno-Mateos, M.A., Vejnar, C.E., Beaudoin, J.-D., Fernandez, J.P., Mis, E.K., Khokha, M.K., and Giraldez, A.J. (2015). CRISPRscan: Designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo. Nat. Methods PMID:26322.
Newmark, P.A., Reddien, P.W., Cebria, F., and Alvarado, A.S. (2003). Ingestion of bacterially expressed double-stranded RNA inhibits gene expression in planarians. Proc. Natl. Acad. Sci. 100, 11861–11865.
Nishiyama, A., and Fujiwara, S. (2008). RNA interference by expressing short hairpin RNA in the Ciona intestinalis embryo. Dev. Growth. Differ. 50, 521–529.
Özpolat, B.D., and Bely, A.E. (2016). Developmental and molecular biology of annelid regeneration: a comparative review of recent studies. Curr. Opin. Genet. Dev. 40, 144–153.
Özpolat, B.D., Handberg-thorsager, M., Vervoort, M., and Balavoine, G. (2017). Cell lineage and cell cycling analyses of the 4d micromere using live imaging in the marine annelid Platynereis dumerilii. Elife, 1–35.
Perry, K.J., and Henry, J.Q. (2015). Technology Report CRISPR / Cas9-Mediated Genome Modification in the Mollusc, Crepidula fornicata. 244, 237–244.
Riley, M., and Vermerris, W. (2017). Recent Advances in Nanomaterials for Gene Delivery—A Review. Nanomaterials 7, 94.
Shaikh, N., Gates, P.B., and Brockes, J.P. (2011). The Meis homeoprotein regulates the axolotl Prod 1 promoter during limb regeneration. Gene 484, 69–74.
Srivastava, M., Mazza-Curll, K.L., van Wolfswinkel, J.C., and Reddien, P.W. (2014). Whole-body acoel regeneration is controlled by Wnt and Bmp-Admp signaling. Curr. Biol. 24, 1107–1113.
Suzuki, K., Tsunekawa, Y., Hernandez-Benitez, R., Wu, J., Zhu, J., Kim, E.J., Hatanaka, F., Yamamoto, M., Araoka, T., Li, Z., Kurita, M., Hishida, T., Li, M., Aizawa, E., Guo, S., Chen, S., Goebl, A., Soligalla, R.D., Qu, J., Jiang, T., Fu, X., Jafari, M., Esteban, C., Berggren, W. T., Lajara, J., Nuñez-Delicado, E., Guillen, P., Campistol, J. M., Matsuzaki, F., Liu, G. H., Magistretti, P., Zhang, K., Callaway, E. M., Zhang, K., and Belmonte, J. C. I. (2016). In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540, 144–149.
Thummel, R., Bai, S., Sarras, M.P., Song, P., Mcdermott, J., Brewer, J., Perry, M., Zhang, X., Hyde, D.R., and Godwin, A.R. (2006). Inhibition of zebrafish fin regeneration using in vivo electroporation of morpholinos against fgfr1 and msxb. 336–346.
Wang, M., Zuris, J.A., Meng, F., Rees, H., Sun, S., Deng, P., Han, Y., Gao, X., Pouli, D., Wu, Q., Georgakoudi, I., Liu, D.R., and Xu, Q. (2016). Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles. Proc. Natl. Acad. Sci. 113, 2868–2873.
Zantke, J., Bannister, S., Veedin Rajan, V.B., Raible, F., and Tessmar-Raible, K. (2014). Genetic and genomic tools for the marine annelid Platynereis dumerilii. Genetics 197, 19–31.
Zuris, J.A., Thompson, D.B., Shu, Y., Guilinger, J.P., Bessen, J.L., Hu, J.H., Maeder, M.L., Joung, J.K., Chen, Z.-Y., and Liu, D.R. (2015). Efficient delivery of genome-editing proteins in vitro and in vivo. Nat Biotechnol 33, 73–80.
Some common approaches to deliver reagents into organisms and their cells include:
- microinjection
- electroporation
- lipofection
- viral delivery
- biolistics
Molecular manipulations
Some common approaches to manipulate gene function include:
- siRNA
- shRNA
- morpholinos
- genome editing
References
Some potentially useful references are below. (Have suggestions for other good references to post here? Please email to let us know!)
Adams, S., Pathak, P., Shao, H., Lok, J.B., and Pires-dasilva, A. (2019). Liposome-based transfection enhances RNAi and CRISPR- mediated mutagenesis in non- model nematode systems. Sci. Rep., 1–12.
Bannister, S., Antonova, O., Polo, A., Lohs, C., Hallay, N., Valinciute, A., Raible, F., and Tessmar-Raible, K. (2014). TALENs mediate efficient and heritable mutation of endogenous genes in the marine annelid Platynereis dumerilii. Genetics 197, 77–89.
Bezares-Calderon, L.A., Berger, J., Jasek, S., Veraszto, C., Mendes, S., Guhmann, M., Almeda, R., Shahidi, R., and Jekely, G. (2018). Neural circuitry of a polycystin-mediated hydrodynamic startle response for predator avoidance. Elife 7, 1–28.
Blum, M., De Robertis, E.M., Wallingford, J.B., and Niehrs, C. (2015). Morpholinos: Antisense and Sensibility. Dev. Cell 35, 145–149.
Chen, S., Lee, B., Lee, A.Y.F., Modzelewski, A.J., and He, L. (2016). Highly efficient mouse genome editing by CRISPR ribonucleoprotein electroporation of zygotes. J. Biol. Chem. 291, 14457–14467.
Conzelmann, M., Williams, E.A., Tunaru, S., Randel, N., Shahidi, R., Asadulina, A., Berger, J., Offermanns, S., and Jekely, G. (2013). Conserved MIP receptor-ligand pair regulates Platynereis larval settlement. Proc Natl Acad Sci U S A 110, 8224–8229.
Cwetsch, A.W., Pinto, B., Savardi, A., and Cancedda, L. (2018). Progress in Neurobiology In vivo methods for acute modulation of gene expression in the central nervous system. Prog. Neurobiol. 168, 69–85.
Demilly, A., Steinmetz, P., Gazave, E., Marchand, L., and Vervoort, M. (2013). Involvement of the Wnt/B-catenin pathway in neurectoderm architecture in Platynereis dumerilii. Nat. Commun. 4, 1911–1915.
Falk, J., Drinjakovic, J., Leung, K.M., Dwivedy, A., Regan, A.G., Piper, M., and Holt, C.E. (2007). Electroporation of cDNA / Morpholinos to targeted areas of embryonic CNS in Xenopus. 16, 1–16.
Fei, J., Knapp, D., Schuez, M., Murawala, P., Zou, Y., Singh, S.P., Drechsel, D., and Tanaka, E.M. (2016). Tissue- and time-directed electroporation of CAS9 protein – gRNA complexes in vivo yields ef fi cient multigene knockout for studying gene function in regeneration. 1–9.
Finn, J.D., Smith, A.R., Patel, M.C., Strapps, W.R., Chang, Y., Morrissey, D. V, Finn, J.D., Smith, A.R., Patel, M.C., Shaw, L., Youniss, M.R., Heteren, J. Van, Dirstine, T., Ciullo, C., Lescarbeau, R., Seitzer, J., Shah, R.R., Shah, A., Ling, D., Growe, J., Pink, M., Rohde, E., Wood, K. M.,
Salomon, W. E., Harrington, W. F., Dombrowski, C., Strapps, W. R., Chang, Y., and Morrissey, D. V. (2018). Report A Single Administration of CRISPR / Cas9 Lipid Nanoparticles Achieves Robust and Persistent In Vivo Genome Editing Report A Single Administration of CRISPR / Cas9 Lipid Nanoparticles Achieves Robust and Persistent In Vivo Genome Editing. CellReports 22, 2227–2235.
Flowers, G.P., Timberlake, A.T., Mclean, K.C., Monaghan, J.R., and Crews, C.M. (2014). Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease. 2165–2171.
Gandhi, S., Piacentino, M.L., Vieceli, F.M., and Bronner, M.E. (2017). Optimization of CRISPR/Cas9 genome editing for loss-of-function in the early chick embryo. Dev. Biol. 432, 86–97.
Genikhovich, G., Fried, P., Iber, D., and Technau, U. (2015). Axis Patterning by BMPs : Cnidarian Network Reveals Report Axis Patterning by BMPs : Cnidarian Network Reveals Evolutionary Constraints. Cell Rep., 1646–1654.
González-Estévez, C., Momose, T., Gehring, W.J., and Saló, E. (2003). Transgenic planarian lines obtained by electroporation using transposon-derived vectors and an eye-specific GFP marker. Proc. Natl. Acad. Sci. U. S. A. 100, 14046–14051.
Grillo, M., Konstantinides, N., and Averof, M. (2016). Old questions, new models: Unraveling complex organ regeneration with new experimental approaches. Curr. Opin. Genet. Dev. 40, 23–31.
Hajj, K.A., and Whitehead, K.A. (2017). Tools for translation: Non-viral materials for therapeutic mRNA delivery. Nat. Rev. Mater. 2, 1–17.
Hashimoto, M., and Takemoto, T. (2015). Electroporation enables the efficient mRNA delivery into the mouse zygotes and facilitates CRISPR/Cas9-based genome editing. Sci. Rep. 5, 1–3.
He, Z.Y., Men, K., Qin, Z., Yang, Y., Xu, T., and Wei, Y.Q. (2017). Non-viral and viral delivery systems for CRISPR-Cas9 technology in the biomedical field. Sci. China Life Sci. 60, 458–467.
Ikmi, A., Mckinney, S.A., Delventhal, K.M., and Gibson, M.C. (2014). TALEN and CRISPR/Cas9-mediated genome editing in the early-branching metazoan Nematostella vectensis. Nat. Commun. 5, 1–8.
Kanasty, R., Dorkin, J.R., Vegas, A., and Anderson, D. (2013). Delivery materials for siRNA therapeutics. Nat. Mater. 12, 967–977.
Kaneko, T., Sakuma, T., Yamamoto, T., and Mashimo, T. (2014). Simple knockout by electroporation of engineered endonucleases into intact rat embryos. Sci. Rep. 4, 1–5.
Karabulut, A., He, S., Chen, C., Mckinney, S.A., Matthew, C., and Gibson, M.C. (2018). Electroporation of short hairpin RNAs for rapid and efficient gene knockdown in the starlet sea anemone , Nematostella vectensis.
Klann, M., and Seaver, E.C. (2018). Functional role of pax6 in eye and central nervous system development in the annelid Capitella teleta. bioRxiv doi.org/10.1101/481135.
Lanza, A.R., and Seaver, E.C. (2018). An organizing role for the TGF-β signaling pathway in axes formation of the annelid Capitella teleta. Dev. Biol. 435, 26–40.
Lee, K., Conboy, M., Park, H.M., Jiang, F., Kim, H.J., Dewitt, M.A., Mackley, V.A., Chang, K., Rao, A., Skinner, C., Shobha, T., Mehdipour, M., Liu, H., Huang, W.C., Lan, F., Bray, N.L., Li, S., Corn, J.E., Kataoka, K., Doudna, J. A., Conboy, I., and Murthy, N. (2017). Nanoparticle delivery of Cas9 ribonucleoprotein and donor DNA in vivo induces homology-directed DNA repair. Nat. Biomed. Eng. 1, 889–901.
Liu, W., Wang, Y., Sun, Y., Wang, Y., Wang, Y., Chen, S., and Zhu, Z. (2005). Efficient RNA interference in zebrafish embryos using siRNA synthesized with SP6 RNA polymerase. 323–331.
Meyer, N.P., Boyle, M.J., Martindale, M.Q., and Seaver, E.C. (2010). A comprehensive fate map by intracellular injection of identified blastomeres in the marine polychaete Capitella teleta. Evodevo 1, 8.
Miura, H., Quadros, R.M., Gurumurthy, C.B., and Ohtsuka, M. (2018). Easi-CRISPR for creating knock-in and conditional knockout mouse models using long ssDNA donors. Nat. Protoc. 13, 195–215.
Moreno-Mateos, M.A., Vejnar, C.E., Beaudoin, J.-D., Fernandez, J.P., Mis, E.K., Khokha, M.K., and Giraldez, A.J. (2015). CRISPRscan: Designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo. Nat. Methods PMID:26322.
Newmark, P.A., Reddien, P.W., Cebria, F., and Alvarado, A.S. (2003). Ingestion of bacterially expressed double-stranded RNA inhibits gene expression in planarians. Proc. Natl. Acad. Sci. 100, 11861–11865.
Nishiyama, A., and Fujiwara, S. (2008). RNA interference by expressing short hairpin RNA in the Ciona intestinalis embryo. Dev. Growth. Differ. 50, 521–529.
Özpolat, B.D., and Bely, A.E. (2016). Developmental and molecular biology of annelid regeneration: a comparative review of recent studies. Curr. Opin. Genet. Dev. 40, 144–153.
Özpolat, B.D., Handberg-thorsager, M., Vervoort, M., and Balavoine, G. (2017). Cell lineage and cell cycling analyses of the 4d micromere using live imaging in the marine annelid Platynereis dumerilii. Elife, 1–35.
Perry, K.J., and Henry, J.Q. (2015). Technology Report CRISPR / Cas9-Mediated Genome Modification in the Mollusc, Crepidula fornicata. 244, 237–244.
Riley, M., and Vermerris, W. (2017). Recent Advances in Nanomaterials for Gene Delivery—A Review. Nanomaterials 7, 94.
Shaikh, N., Gates, P.B., and Brockes, J.P. (2011). The Meis homeoprotein regulates the axolotl Prod 1 promoter during limb regeneration. Gene 484, 69–74.
Srivastava, M., Mazza-Curll, K.L., van Wolfswinkel, J.C., and Reddien, P.W. (2014). Whole-body acoel regeneration is controlled by Wnt and Bmp-Admp signaling. Curr. Biol. 24, 1107–1113.
Suzuki, K., Tsunekawa, Y., Hernandez-Benitez, R., Wu, J., Zhu, J., Kim, E.J., Hatanaka, F., Yamamoto, M., Araoka, T., Li, Z., Kurita, M., Hishida, T., Li, M., Aizawa, E., Guo, S., Chen, S., Goebl, A., Soligalla, R.D., Qu, J., Jiang, T., Fu, X., Jafari, M., Esteban, C., Berggren, W. T., Lajara, J., Nuñez-Delicado, E., Guillen, P., Campistol, J. M., Matsuzaki, F., Liu, G. H., Magistretti, P., Zhang, K., Callaway, E. M., Zhang, K., and Belmonte, J. C. I. (2016). In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration. Nature 540, 144–149.
Thummel, R., Bai, S., Sarras, M.P., Song, P., Mcdermott, J., Brewer, J., Perry, M., Zhang, X., Hyde, D.R., and Godwin, A.R. (2006). Inhibition of zebrafish fin regeneration using in vivo electroporation of morpholinos against fgfr1 and msxb. 336–346.
Wang, M., Zuris, J.A., Meng, F., Rees, H., Sun, S., Deng, P., Han, Y., Gao, X., Pouli, D., Wu, Q., Georgakoudi, I., Liu, D.R., and Xu, Q. (2016). Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles. Proc. Natl. Acad. Sci. 113, 2868–2873.
Zantke, J., Bannister, S., Veedin Rajan, V.B., Raible, F., and Tessmar-Raible, K. (2014). Genetic and genomic tools for the marine annelid Platynereis dumerilii. Genetics 197, 19–31.
Zuris, J.A., Thompson, D.B., Shu, Y., Guilinger, J.P., Bessen, J.L., Hu, J.H., Maeder, M.L., Joung, J.K., Chen, Z.-Y., and Liu, D.R. (2015). Efficient delivery of genome-editing proteins in vitro and in vivo. Nat Biotechnol 33, 73–80.