TILLING: practical single-nucleotide mutation discovery.

In the post-genomic sequencing era, an expanding portfolio of genomic technologies has been applied to the study of gene function. Reverse genetics approaches that provide targeted inactivation of genes identified by sequence analysis include TILLING (for Targeting Local Lesions IN Genomes). TILLING searches the genomes of mutagenized organisms for mutations in a chosen gene, typically single base-pair substitutions. This review covers practical aspects of the technology, ranging from building the mutagenized population to mutation discovery, and discusses possible improvements to current protocols and the impact of new genomic methods for mutation discovery in relation to the future of the TILLING approach.

[1]  D. Stemple.  TILLING — a high-throughput harvest for functional genomics , 2004, Nature Reviews Genetics.

[2]  J. Durocher,et al.  Mutation detection using Surveyor nuclease. , 2004, BioTechniques.

[3]  C. Miller,et al.  Purification, cloning, and characterization of the CEL I nuclease. , 2000, Biochemistry.

[4]  Steven Henikoff,et al.  Mismatch cleavage by single-strand specific nucleases. , 2004, Nucleic acids research.

[5]  M. Laskowski,et al.  Mung bean nuclease I. Terminally directed hydrolysis of native DNA. , 1976, Biochemistry.

[6]  C. McCallum,et al.  A high-throughput method for identifying N-ethyl-N-nitrosourea (ENU)-induced point mutations in zebrafish. , 2004, Methods in cell biology.

[7]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[8]  R. Cotton,et al.  The use of resolvases T4 endonuclease VII and T7 endonuclease I in mutation detection , 2003, Molecular biotechnology.

[9]  Franco Cerrina,et al.  Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. , 2002, Genome research.

[10]  B. Kemper,et al.  Detection of 81 of 81 known mouse beta-globin promoter mutations with T4 endonuclease VII--the EMC method. , 1996, Genomics.

[11]  V. Knauf,et al.  TILLING moves beyond functional genomics into crop improvement , 2005, Transgenic Research.

[12]  P. Vos,et al.  AFLP: a new technique for DNA fingerprinting. , 1995, Nucleic acids research.

[13]  Xin Li,et al.  A fast neutron deletion mutagenesis-based reverse genetics system for plants. , 2001, The Plant journal : for cell and molecular biology.

[14]  Jan Leach,et al.  Chemical- and Irradiation-induced Mutants of Indica Rice IR64 for Forward and Reverse Genetics , 2005, Plant Molecular Biology.

[15]  S. Fuerstenberg,et al.  A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING , 2005, Nature Biotechnology.

[16]  Zhaowei Liu,et al.  Integrated platform for detection of DNA sequence variants using capillary array electrophoresis , 2002, Electrophoresis.

[17]  R. Goldsby,et al.  High incidence of epithelial cancers in mice deficient for DNA polymerase δ proofreading , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Kazuo Yamamoto,et al.  Escherichia coli mutator (Delta)polA is defective in base mismatch correction: the nature of in vivo DNA replication errors. , 2005, Journal of molecular biology.

[19]  S. Henikoff,et al.  Single-nucleotide mutations for plant functional genomics. , 2003, Annual review of plant biology.

[20]  M. Rieder,et al.  Sequence-based detection of single nucleotide polymorphisms. , 2001, Methods in molecular biology.

[21]  S. Henikoff,et al.  TILLING. Traditional Mutagenesis Meets Functional Genomics , 2004, Plant Physiology.

[22]  R. Strausberg,et al.  High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Naama Menda,et al.  In silico screening of a saturated mutation library of tomato. , 2004, The Plant journal : for cell and molecular biology.

[24]  S. Henikoff,et al.  Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. , 2004, The Plant journal : for cell and molecular biology.

[25]  G. Haughn,et al.  TILLING without a plough: a new method with applications for reverse genetics. , 2005, Current opinion in plant biology.

[26]  J. Shendure,et al.  Materials and Methods Som Text Figs. S1 and S2 Tables S1 to S4 References Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2022 .

[27]  S. Henikoff,et al.  Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. , 2003, Genetics.

[28]  Nicholas E. Taylor,et al.  PARSESNP: a tool for the analysis of nucleotide polymorphisms , 2003, Nucleic Acids Res..

[29]  S. Henikoff,et al.  High-throughput TILLING for functional genomics. , 2003, Methods in molecular biology.

[30]  Steven Henikoff,et al.  Large-scale discovery of induced point mutations with high-throughput TILLING. , 2003, Genome research.

[31]  A Chakravarti,et al.  High-throughput variation detection and genotyping using microarrays. , 2001, Genome research.

[32]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[33]  E. Gross,et al.  A comparison of BRCA1 mutation analysis by direct sequencing, SSCP and DHPLC , 1999, Human Genetics.

[34]  R. W. Davis,et al.  Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. , 1997, Genome research.

[35]  C. Schutt,et al.  Novel sulfoxides facilitate GC-rich template amplification. , 2002, BioTechniques.

[36]  Nathan M. Springer,et al.  Discovery of induced point mutations in maize genes by TILLING , 2004, BMC Plant Biology.

[37]  Jeffrey C. Miller,et al.  Highly efficient endogenous human gene correction using designed zinc-finger nucleases , 2005, Nature.

[38]  R. Cotton,et al.  The use of chemical reagents in the detection of DNA mutations. , 1993, Mutation research.

[39]  A. Godwin,et al.  Mutation detection using a novel plant endonuclease. , 1998, Nucleic acids research.

[40]  Steven Henikoff,et al.  Targeted screening for induced mutations , 2000, Nature Biotechnology.

[41]  C. Dearolf,et al.  Targeted recovery of mutations in Drosophila. , 2000, Genetics.

[42]  Martin Parniske,et al.  A TILLING Reverse Genetics Tool and a Web-Accessible Collection of Mutants of the Legume Lotus japonicus 1 , 2003, Plant Physiology.

[43]  S. Henikoff,et al.  High-throughput screening for induced point mutations. , 2001, Plant physiology.

[44]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.

[45]  M. Mayhaus,et al.  Efficient and fast targeted production of murine models based on ENU mutagenesis , 2005, Mammalian Genome.

[46]  E. Cuppen,et al.  Target-selected mutagenesis of the rat. , 2004, Genomics.

[47]  M. Ronaghi,et al.  Genetic variation analyses by Pyrosequencing. , 2005, Mutation research.

[48]  P. Oefner,et al.  Temperature-modulated array high-performance liquid chromatography. , 2001, Genome research.

[49]  S. Lory,et al.  Detection of simple mutations and polymorphisms in large genomic regions. , 2001, Nucleic acids research.

[50]  D. Lawlor,et al.  Mutation scanning by meltMADGE: validations using BRCA1 and LDLR, and demonstration of the potential to identify severe, moderate, silent, rare, and paucimorphic mutations in the general population. , 2005, Genome research.

[51]  K. Gunderson,et al.  A genome-wide scalable SNP genotyping assay using microarray technology , 2005, Nature Genetics.

[52]  C. van Broeckhoven,et al.  novoSNP, a novel computational tool for sequence variation discovery. , 2005, Genome research.

[53]  V. Shankar,et al.  Single-strand-specific nucleases. , 2003, FEMS microbiology reviews.

[54]  S. Henikoff,et al.  Automated band mapping in electrophoretic gel images using background information , 2005, Nucleic acids research.

[55]  M. Neff,et al.  Web-based primer design for single nucleotide polymorphism analysis. , 2002, Trends in genetics : TIG.

[56]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[57]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[58]  S. Otto,et al.  Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa , 2006, Molecular ecology.

[59]  L. Stadler.  CHROMOSOME NUMBER AND THE MUTATION RATE IN AVENA AND TRITICUM. , 1929, Proceedings of the National Academy of Sciences of the United States of America.

[60]  Paul D. Shaw,et al.  A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). , 2004, The Plant journal : for cell and molecular biology.

[61]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[62]  Edwin Cuppen,et al.  Efficient target-selected mutagenesis in zebrafish. , 2003, Genome research.

[63]  P Berg,et al.  Biochemical method for mapping mutational alterations in DNA with S1 nuclease: the location of deletions and temperature-sensitive mutations in simian virus 40. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[64]  M. Gonzalez-Gaitan,et al.  Target-selected mutant screen by TILLING in Drosophila. , 2005, Genome research.