TILLING: Practical single-nucleotide mutation discovery

Plant Journal

Volumn 45, Issue 4, 2006, Pages 684-694

  Comai, Luca ^a   Henikoff, Steven ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Gel electrophoresis; Mismatch cleavage; Mutagenesis; Mutation discovery; Polymorphism detection

Indexed keywords

ELECTROPHORESIS; GELS; NUCLEIC ACID SEQUENCES;

GEL ELECTROPHORESIS; MISMATCH CLEAVAGE; MUTATION DISCOVERY; POLYMORPHISM DETECTION;

MUTAGENESIS;

MUTATION; POLYMERASE CHAIN REACTION; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

MUTATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE;

ELECTROPHORESIS; GELS; GENETIC ENGINEERING;

EID: 33644865733     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2006.02670.x     Document Type: Review

References (65)

1. Alharbi K.K. Aldahmesh M.A Spanakis E. et al. 2005 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 Genome Res. 15 967 977
2. Altschul S.F Madden T.L. Schaffer A.A. Zhang J. Zhang Z. Miller W. Lipman D.J. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 3389 3402
3. Augustin M. Sedlmeier R. Peters T. et al. 2005 Efficient and fast targeted production of murine models based on ENU mutagenesis. Mamm Genome. 16 405 413
4. Babon J.J. McKenzie M. Cotton R.G. 2003 The use of resolvases T4 endonuclease VII and T7 endonuclease I in mutation detection Mol. Biotechnol. 23 73 81
5. Bentley A. MacLennan B. Calvo J. Dearolf C.R. 2000 Targeted recovery of mutations in Drosophila Genetics 156 1169 1173
6. Buetow K.H. Edmonson M. MacDonald R. et al. 2001 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 Proc. Natl Acad. Sci. USA 98 581 584
7. Caldwell D.G. McCallum N. Shaw P. Muehlbauer G.J. Marshall D.F. Waugh R. 2004 A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.) Plant J. 40 143 150
8. Chakrabarti R. Schutt C.E. 2002 Novel sulfoxides facilitate GC-rich template amplification Biotechniques 32 866 868 870 866 862 874
9. Colbert T. Till B.J. Tompa R. Reynolds S. Steine M.N. Yeung A.T. McCallum C.M. Comai L. Henikoff S. 2001 High-throughput screening for induced point mutations Plant Physiol. 126 480 484
10. Comai L. Young K. Till B.J. et al. 2004 Efficient discovery of DNA polymorphisms in natural populations by Ecotilling Plant J. 37 778 786
11. Cutler D.J. Zwick M.E. Carrasquillo M.M. et al. 2001 High-throughput variation detection and genotyping using microarrays Genome Res. 11 1913 1925
12. Desai N.A. Shankar V. 2003 Single-strand-specific nucleases FEMS Microbiol. Rev. 26 457 491
13. Draper B.W. McCallum C.M. Stout J.L. Slade A.J. Moens C.B. 2004 A high-throughput method for identifying N-ethyl-N-nitrosourea (ENU)-induced point mutations in zebrafish Methods Cell Biol. 77 91 112
14. Gilchrist E.J. Haughn G.W. 2005 TILLING without a plough: a new method with applications for reverse genetics Curr. Opin. Plant Biol. 8 211 215
15. Gilchrist E.J. Haughn G.W. Ying C.C. et al. 2006 Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa Mol. Ecol. (in press)
16. Goldsby R.E. Hays L.E. Chen X. Olmsted E.A. Slayton W.B. Spangrude G.J. Preston B.D. 2002 High incidence of epithelial cancers in mice deficient for DNA polymerase delta proofreading Proc. Natl Acad. Sci. USA 99 15560 15565
17. Greene E.A. Codomo C.A. Taylor N.E. et al. 2003 Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis Genetics 164 731 740
18. Gross E. Arnold N. Goette J. Schwarz-Boeger U. Kiechle M. 1999 A comparison of BRCA1 mutation analysis by direct sequencing, SSCP and DHPLC Hum. Genet. 105 72 78
19. Gunderson K.L. Steemers F.J. Lee G. Mendoza L.G. Chee M.S. 2005 A genome-wide scalable SNP genotyping assay using microarray technology Nat. Genet. 37 549 554
20. Henikoff S. Comai L. 2003 Single-nucleotide mutations for plant functional genomics Annu. Rev. Plant Biol. 54 375 401
21. Henikoff S. Till B.J. Comai L. 2004 TILLING. Traditional mutagenesis meets functional genomics Plant Physiol. 135 630 636
22. Hughes T.R. Hughes T.R. Hughes T.R. et al. 2001 Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer Nat. Biotechnol. 19 342 347
23. Kroeker W.D. Kowalski D. Laskowski M.S. 1976 Mung bean nuclease I. Terminally directed hydrolysis of native DNA Biochemistry 15 4463 4467
24. Lander E.S. Linton L.M. Birren B. et al. 2001 Initial sequencing and analysis of the human genome Nature 409 860 921
25. Langaee T. Ronaghi M. 2005 Genetic variation analyses by Pyrosequencing Mutat. Res. 573 96 102
26. Li X. Song Y. Century K. Straight S. Ronald P. Dong X. Lassner M. Zhang Y. 2001 A fast neutron deletion mutagenesis-based reverse genetics system for plants Plant J. 27 235 242
27. Li Q. Liu Z. Monroe H. Culiat C.T. 2002 Integrated platform for detection of DNA sequence variants using capillary array electrophoresis Electrophoresis 23 1499 1511
28. Margulies M. Egholm M. Altman W.E. et al. 2005 Genome sequencing in microfabricated high-density picolitre reactors Nature 437 376 380
29. McCallum C.M. Comai L. Greene E.A. Henikoff S. 2000 Targeted screening for induced mutations Nat. Biotechnol. 18 455 457
30. Menda N. Semel Y. Peled D. Eshed Y. Zamir D. 2004 In silico screening of a saturated mutation library of tomato Plant J. 38 861 872
31. Neff M.M. Turk E. Kalishman M. 2002 Web-based primer design for single nucleotide polymorphism analysis Trends Genet. 18 613 615
32. Nickerson D.A. Kolker N. Taylor S.L. Rieder M.J. 2001 Sequence-based detection of single nucleotide polymorphisms Methods Mol. Biol. 175 29 35
33. Nuwaysir E.F. Huang W. Albert T.J. et al. 2002 Gene expression analysis using oligonucleotide arrays produced by maskless photolithography Genome Res. 12 1749 1755
34. Oleykowski C.A. Bronson Mullins C.R. Godwin A.K. Yeung A.T. 1998 Mutation detection using a novel plant endonuclease Nucleic Acids Res. 26 4597 4602
35. Perry J.A. Wang T.L. Welham T.J. Gardner S. Pike J.M. Yoshida S. Parniske M. 2003 A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus Plant Physiol. 131 866 871
36. Premstaller A. Xiao W. Oberacher H. O'Keefe M. Stern D. Willis T. Huber C.G. Oefner P.J. 2001 Temperature-modulated array high-performance liquid chromatography Genome Res. 11 1944 1951
37. Qiu P. Shandilya H. D'Alessio J.M. O'Connor K. Durocher J. Gerard G.F. 2004 Mutation detection using Surveyor nuclease Biotechniques 36 702 707
38. Rozen S. Skaletsky H. 2000 Primer3 on the WWW for general users and for biologist programmers Methods Mol. Biol. 132 365 386
39. Shendure J. Porreca G.J. Reppas N.B. Lin X. McCutcheon J.P. Rosenbaum A.M. Wang M.D. Zhang K. Mitra R.D. Church G.M. 2005 Accurate multiplex polony sequencing of an evolved bacterial genome Science 309 1728 1732
40. Shenk T.E. Rhodes C. Rigby P.W. Berg P. 1975 Biochemical method for mapping mutational alterations in DNA with S1 nuclease: the location of deletions and temperature-sensitive mutations in simian virus 40 Proc. Natl Acad. Sci. USA 72 989 993
41. Slade A.J. Knauf V.C. 2005 TILLING moves beyond functional genomics into crop improvement Transgenic Res. 14 109 115
42. Slade A.J. Fuerstenberg S.I. Loeffler D. Steine M.N. Facciotti D. 2005 A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING Nat. Biotechnol. 23 75 81
43. Smits B.M. Mudde J. Plasterk R.H. Cuppen E. 2004 Target-selected mutagenesis of the rat Genomics 83 332 334
44. Smooker P.M. Cotton R.G. 1993 The use of chemical reagents in the detection of DNA mutations Mutat. Res. 288 65 77
45. Sokurenko E.V. Tchesnokova V. Yeung A.T. Oleykowski C.A. Trintchina E. Hughes K.T. Rashid R.A. Brint J.M. Moseley S.L. Lory S. 2001 Detection of simple mutations and polymorphisms in large genomic regions Nucleic Acids Res. 29 E111
46. Stadler I.J. 1929 Chromosome number and the mutation rate in Avena and Triticum Proc. Natl Acad. Sci. USA 15 876 881
47. Stemple D.L. 2004 TILLING - a high-throughput harvest for functional genomics Nat. Rev. Genet. 5 145 150
48. Tago Y. Imai M. Ihara M. Atofuji H. Nagata Y. Yamamoto K. 2005 Escherichia coli mutator (Delta)polA is defective in base mismatch correction: the nature of in vivo DNA replication errors J. Mol. Biol. 351 299 308
49. Taylor N.E. Greene E.A. 2003 PARSESNP: a tool for the analysis of nucleotide polymorphisms Nucleic Acids Res. 31 3808 3811
50. Till B.J. Colbert T. Tompa R. et al. 2003a High-throughput TILLING for functional genomics Methods Mol. Biol. 236 205 220
51. Till B.J. Reynolds S.H. Greene E.A. et al. 2003b Large-scale discovery of induced point mutations with high-throughput TILLING Genome Res. 13 524 530
52. Till B.J. Burtner C. Comai L. Henikoff S. 2004a q50 Mismatch cleavage by single-strand specific nucleases Nucleic Acids Res. 32 2632 2641
53. Till B.J. Reynolds S.H. Weil C. et al. 2004b q51 Discovery of induced point mutations in maize genes by TILLING BMC Plant Biol. 4 12
54. Underhill P.A. Jin L. Lin A.A. Mehdi S.Q. Jenkins T. Vollrath D. Davis R.W. Cavalli-Sforza L.L. Oefner P.J. 1997 Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography Genome Res. 7 10 996 1005
55. Urnov F.D. Miller J.C. Lee Y.L. Beausejour C.M. Rock J.M. Augustus S. Jamieson A.C. Porteus M.H. Gregory P.D. Holmes M.C. 2005 Highly efficient endogenous human gene correction using designed zinc-finger nucleases Nature 435 646 651
56. Venter J.C. Adams M.D. Myers E.W. et al. 2001 The sequence of the human genome Science 291 1304 1351
57. Vos P. Hogers R. Bleeker M. et al. 1995 AFLP: a new technique for DNA fingerprinting Nucleic Acids Res. 23 4407 4414
58. Wagner R. Dean A. 2000 The use of immobilized mismatch binding protein in mutation/SNP detection Methods Mol. Biol. 152 159 168
59. Weckx S. Del-Favero J. Rademakers R. Claes L. Cruts M. De Jonghe P. Van Broeckhoven C. De Rijk P. 2005 novoSNP, a novel computational tool for sequence variation discovery Genome Res. 15 436 442
60. Wienholds E. van Eeden F. Kosters M. Mudde J. Plasterk R.H. Cuppen E. 2003 Efficient target-selected mutagenesis in zebrafish Genome Res. 13 2700 2707
61. Winkler S. Schwabedissen A. Backasch D. et al. 2005 Target-selected mutant screen by TILLING in Drosophila Genome Res. 15 718 723
62. Wu J.L. Wu C. Lei C. et al. 2005 Chemical- and irradiation-induced mutants of Indica Rice IR64 for forward and reverse genetics Plant Mol. Biol. 59 85 97
63. Yang B. Wen X. Kodali N.S. Oleykowski C.A. Miller C.G. Kulinski J. Besack D. Yeung J.A. Kowalski D. Yeung A.T. 2000 Purification, cloning, and characterization of the CEL I nuclease Biochemistry 39 3533 3541
64. Youil R. Kemper B. Cotton R.G. 1996 Detection of 81 of 81 known mouse beta-globin promoter mutations with T4 endonuclease VII - the EMC method Genomics 32 431 435
65. Zerr T. Henikoff S. 2005 Automated band mapping in electrophoretic gel images using background information Nucleic Acids Res. 33 2806 2812