Abstract
TILLING (Targeting Induced Local Lesions IN Genomes) is a popular reverse genetic approach that has been successfully applied in several genetic model organisms such as zebrafish, rat, Drosophila, Arabidopsis, or medaka. In contrast to classical targeted knockout technologies that work in mice by directly targeting a gene of interest, TILLING follows an indirect strategy. The first step of the TILLING pipeline is the generation of a TILLING library that consists of large numbers of mutagenized individuals. In a second step, these individuals are screened for mutations in any gene of interest. Screening is performed by PCR amplification of specific exons from each individual of a library followed by mutation detection. This could be done, for example, by direct re-sequencing of PCR fragments or alternatively, by CEL1 endonuclease-mediated mutation discovery. Individuals carrying potentially deleterious point mutations are isolated from the library and mutant lines are established. TILLING allows the identification of a whole range of point mutations, covering nonsense, splice site, and missense mutations in only one screening round, because the generation of mutations by mutagenesis as well as the screening tools is not biased. Potential knockout mutations are initially the mutations of choice, but TILLING screens can also be used to isolate allelic series of point mutations ranging from complete null phenotypes to hypomorphic or even dominant-negative or conditional alleles. These allelic series can be helpful for a comprehensive functional analysis of a gene of interest. TILLING is applicable to any kind of genetically tractable model organism, as long as this model organism is amenable to chemical mutagenesis, and genomic sequence information for a gene of interest is available. This chapter describes the design and pipeline of a TILLING facility as we are currently operating it for zebrafish in Dresden. Protocols for mutation detection by direct re-sequencing are described in detail. However, alternatives to this pipeline do exist and will be mentioned briefly.
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References
Colbert, T., Till, B. J., Tompa, R., Reynolds, S., Steine, M. N., Yeung, A. T., McCallum, C. M., Comai, L., and Henikoff, S. (2001) High-throughput screening for induced point mutations. Plant Physiol. 126, 480–484.
McCallum, C. M., Comai, L., Greene, E. A., and Henikoff, S. (2000) Targeted screening for induced mutations. Nat Biotechnol. 18, 455–457.
Draper, B. W., McCallum, C. M., Stout, J. L., Slade, A. J., Moens, C. B., Draper, B. W., McCallum, C. M., Stout, J. L., Slade, A. J., and Moens, C. B. (2004) A high-throughput method for identifying N-ethyl-N-nitrosourea (ENU)-induced point mutations in zebrafish. Meth. Cell Biol. 77, 91–112.
Wienholds, E., Schulte-Merker, S., Walderich, B., Plasterk, R. H., Wienholds, E., Schulte-Merker, S., Walderich, B., and Plasterk, R. H. A. (2002) Target-selected inactivation of the zebrafish rag1 gene. Science 297, 99–102.
Smits, B. M., Mudde, J., Plasterk, R. H., and Cuppen, E. (2004) Target-selected mutagenesis of the rat. Genomics 83, 332–334.
Taniguchi, Y., Takeda, S., Furutani-Seiki, M., Kamei, Y., Todo, T., Sasado, T., Deguchi, T., Kondoh, H., Mudde, J., Yamazoe, M., Hidaka, M., Mitani, H., Toyoda, A., Sakaki, Y., Plasterk, R. H., Cuppen, E., Taniguchi, Y., Takeda, S., Furutani-Seiki, M., Kamei, Y., Todo, T., Sasado, T., Deguchi, T., Kondoh, H., Mudde, J., Yamazoe, M., Hidaka, M., Mitani, H., Toyoda, A., Sakaki, Y., Plasterk, R. H. A., and Cuppen, E. (2006) Generation of medaka gene knockout models by target-selected mutagenesis. Genome Biol. 7, R116.
Stemple, D. L. and Stemple, D. L. (2004) TILLING--a high-throughput harvest for functional genomics. Nat. Rev. Genet. 5, 145–150.
Wienholds, E., van Eeden, F., Kosters, M., Mudde, J., Plasterk, R. H., Cuppen, E., Wienholds, E., van Eeden, F., Kosters, M., Mudde, J., Plasterk, R. H. A., and Cuppen, E. (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res. 13, 2700–2707.
Moens, C. B., Donn, T. M., Wolf-Saxon, E. R., Ma, T. P., Moens, C. B., Donn, T. M., Wolf-Saxon, E. R., and Ma, T. P. (2008) Reverse genetics in zebrafish by TILLING. Brief. Funct. Genomics Proteomic. 7, 454–459.
Grunwald, D. J. and Streisinger, G. (1992) Induction of recessive lethal and specific locus mutations in the zebrafish with ethyl nitrosourea. Genet. Res. 59, 103–116.
Mullins, M. C., Hammerschmidt, M., Haffter, P., and Nusslein-Volhard, C. (1994) Large-scale mutagenesis in the zebrafish: in search of genes controlling development in a vertebrate. Curr. Biol. 4, 189–202.
Solnica-Krezel, L., Schier, A. F., and Driever, W. (1994) Efficient recovery of ENU-induced mutations from the zebrafish germline. Genetics 136, 1401–1420.
de Bruijn, E., Cuppen, E., Feitsma, H., de Bruijn, E., Cuppen, E., and Feitsma, H. (2009) Highly efficient ENU mutagenesis in zebrafish. Meth. Mol. Biol. 546, 3–12.
Carmichael, C., Westerfield, M., Varga, Z. M., Carmichael, C., Westerfield, M., and Varga, Z. M. (2009) Cryopreservation and in vitro fertilization at the zebrafish international resource center. Meth. Mol. Biol. 546, 45–65.
Till, B. J., Colbert, T., Tompa, R., Enns, L. C., Codomo, C. A., Johnson, J. E., Reynolds, S. H., Henikoff, J. G., Greene, E. A., Steine, M. N., Comai, L., Henikoff, S., Till, B. J., Colbert, T., Tompa, R., Enns, L. C., Codomo, C. A., Johnson, J. E., Reynolds, S. H., Henikoff, J. G., Greene, E. A., Steine, M. N., Comai, L., and Henikoff, S. (2003) High-throughput TILLING for functional genomics. Meth. Mol. Biol. 236, 205–220.
Winkler, S., Schwabedissen, A., Backasch, D., Bokel, C., Seidel, C., Bonisch, S., Furthauer, M., Kuhrs, A., Cobreros, L., Brand, M., Gonzalez-Gaitan, M., Winkler, S., Schwabedissen, A., Backasch, D., Bokel, C., Seidel, C., Bonisch, S., Furthauer, M., Kuhrs, A., Cobreros, L., Brand, M., and Gonzalez-Gaitan, M. (2005) Target-selected mutant screen by TILLING in Drosophila. Genome Res. 15, 718–723.
Sood, R., English, M. A., Jones, M., Mullikin, J., Wang, D. M., Anderson, M., Wu, D., Chandrasekharappa, S. C., Yu, J., Zhang, J., and Paul Liu, P. (2006) Methods for reverse genetic screening in zebrafish by resequencing and TILLING. Methods 39, 220–227.
Bhangale, T. R., Stephens, M., and Nickerson, D. A. (2006) Automating resequencing-based detection of insertion-deletion polymorphisms. Nat. Genet. 38, 1457–1462.
Nickerson, D. A., Tobe, V. O., and Taylor, S. L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745–2751.
Till, B. J., Zerr, T., Comai, L., Henikoff, S., Till, B. J., Zerr, T., Comai, L., and Henikoff, S. (2006) A protocol for TILLING and Ecotilling in plants and animals. Nat. Protoc. 1, 2465–2477.
Uauy, C., Paraiso, F., Colasuonno, P., Tran, R. K., Tsai, H., Berardi, S., Comai, L., and Dubcovsky, J. (2009) A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat. BMC Plant Biol. 9, 115.
Acevedo-Arozena, A., Wells, S., Potter, P., Kelly, M., Cox, R. D., Brown, S. D., Acevedo-Arozena, A., Wells, S., Potter, P., Kelly, M., Cox, R. D., and Brown, S. D. M. (2008) ENU mutagenesis, a way forward to understand gene function. Annu. Rev. Genomics Hum. Genet. 9, 49–69.
Crowe, M. L. (2005) SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms. BMC Bioinformatics 6, 133.
Weckx, S., Del-Favero, J., Rademakers, R., Claes, L., Cruts, M., De Jonghe, P., Van Broeckhoven, C., and De Rijk, P. (2005) novoSNP, a novel computational tool for sequence variation discovery. Genome Res. 15, 436–442.
Zhang, J., Wheeler, D. A., Yakub, I., Wei, S., Sood, R., Rowe, W., Liu, P. P., Gibbs, R. A., and Buetow, K. H. (2005) SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput. Biol. 1, e53.
Neff, M. M., Neff, J. D., Chory, J., and Pepper, A. E. (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J. 14, 387–392.
Neff, M. M., Turk, E., and Kalishman, M. (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet. 18, 613–615.
Bui, M. and Liu, Z. (2009) Simple allele-discriminating PCR for cost-effective and rapid genotyping and mapping. Plant Methods 5, 1.
Acknowledgments
The authors would like to thank Sylvia Schimpke, Katja Steinberg, Claudia Seidel, and Evelin Lehmann for excellent technical support, Julia Jarrells for critical reading of the manuscript, and our collaborators Edwin Cuppen, Victor Guryev, and Ewart de Bruijn (Hubrecht Institute, Utrecht), Derek Stemple, Ross Kettleborough, and Elisabeth Busch-Nentwich (Sanger Institute, Cambridge) for sharing zebrafish TILLING libraries, materials, and protocols. The Dresden TILLING facility is supported by the MPI for Molecular Cell Biology and Genetics in Dresden, the Center for Regenerative Therapies in Dresden, the Biotechnology Center of the Technical University Dresden, and by grants from the European Union to M.B. (Zf Models and Zf Health).
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Winkler, S., Gscheidel, N., Brand, M. (2011). Mutant Generation in Vertebrate Model Organisms by TILLING. In: Pelegri, F. (eds) Vertebrate Embryogenesis. Methods in Molecular Biology, vol 770. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-210-6_19
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DOI: https://doi.org/10.1007/978-1-61779-210-6_19
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