High-resolution melting curve analysis for rapid detection of mutations in a Medaka TILLING library

BMC Molecular Biology

Volumn 11, Issue , 2010, Pages

  Ishikawa, Tomoko ^a   Kamei, Yasuhiro ^a   Otozai, Shinji ^b   Kim, Jinhyong ^a   Sato, Ayuko ^c   Kuwahara, Yoshikazu ^d   Tanaka, Minoru ^e   Deguchi, Tomonori ^f   Inohara, Hidenori ^b   Tsujimura, Tohru ^c   Todo, Takeshi ^a  

^a OSAKA UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^b OSAKA UNIVERSITY MEDICAL SCHOOL   (Japan)

^c HYOGO COLLEGE OF MEDICINE   (Japan)

^d TOHOKU UNIVERSITY   (Japan)

^e NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^f NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ATM PROTEIN; ATR PROTEIN; PROTEIN P53; ALKYLATING AGENT; CELL CYCLE PROTEIN; DNA; DNA BINDING PROTEIN; ETHYLNITROSOUREA; PROTEIN SERINE THREONINE KINASE; TUMOR SUPPRESSOR PROTEIN;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CELL PROLIFERATION; CONTROLLED STUDY; DNA LIBRARY; DNA SEQUENCE; DNA SPLICING; EMBRYO; EXON; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC SCREENING; HIGH RESOLUTION MELTING CURVE ANALYSIS; LOSS OF FUNCTION MUTATION; NONHUMAN; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; ORYZIAS; OUTCOME ASSESSMENT; PHENOTYPE; POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; TARGETING INDUCED LOCAL LESIONS IN GENOMES; AMINO ACID SEQUENCE; ANIMAL; DNA DENATURATION; DRUG EFFECT; FEMALE; GENE LIBRARY; GENETICS; HIGH THROUGHPUT NUCLEOTIDE SEQUENCING; HISTOLOGY; HUMAN; MALE; METHODOLOGY; MOLECULAR GENETICS; MUTAGENESIS; MUTATION; RADIATION EXPOSURE;

ANIMALIA; ORYZIINAE;

ALKYLATING AGENTS; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CELL CYCLE PROTEINS; DNA; DNA MUTATIONAL ANALYSIS; DNA-BINDING PROTEINS; ETHYLNITROSOUREA; FEMALE; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MOLECULAR SEQUENCE DATA; MUTAGENESIS; MUTATION; NUCLEIC ACID DENATURATION; ORYZIAS; PROTEIN-SERINE-THREONINE KINASES; TUMOR SUPPRESSOR PROTEIN P53; TUMOR SUPPRESSOR PROTEINS;

EID: 77956524613     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-11-70     Document Type: Article

References (47)

1. McCallum CM, Comai L, Greene EA, Henikoff S. Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. Plant Physiol 2000, 123(2):439-442. 10.1104/pp.123.2.439, 1539256, 10859174.
2. Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S. High-throughput screening for induced point mutations. Plant Physiol 2001, 126(2):480-484. 10.1104/pp.126.2.480, 1540114, 11402178.
3. Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, et al. Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol 2004, 4:12. 10.1186/1471-2229-4-12, 512284, 15282033.
4. Perry JA, Wang TL, Welham TJ, Gardner S, Pike JM, Yoshida S, Parniske M. A TILLING reverse genetics tool and a web-accessible collection of mutants of the legume Lotus japonicus. Plant Physiol 2003, 131(3):866-871. 10.1104/pp.102.017384, 1540285, 12644638.
5. Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R. A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J 2004, 40(1):143-150. 10.1111/j.1365-313X.2004.02190.x, 15361148.
6. Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D. A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nat Biotechnol 2005, 23(1):75-81. 10.1038/nbt1043, 15580263.
7. Winkler S, Schwabedissen A, Backasch D, Bokel C, Seidel C, Bonisch S, Furthauer M, Kuhrs A, Cobreros L, Brand M, et al. Target-selected mutant screen by TILLING in Drosophila. Genome Res 2005, 15(5):718-723. 10.1101/gr.3721805, 1088300, 15867432.
8. Wienholds E, van Eeden F, Kosters M, Mudde J, Plasterk RH, Cuppen E. Efficient target-selected mutagenesis in zebrafish. Genome Res 2003, 13(12):2700-2707. 10.1101/gr.1725103, 403812, 14613981.
9. Taniguchi Y, Takeda S, Furutani-Seiki M, Kamei Y, Todo T, Sasado T, Deguchi T, Kondoh H, Mudde J, Yamazoe M, et al. Generation of medaka gene knockout models by target-selected mutagenesis. Genome Biol 2006, 7(12):R116. 10.1186/gb-2006-7-12-r116, 1794429, 17156454.
10. Wittbrodt J, Shima A, Schartl M. Medaka--a model organism from the far East. Nat Rev Genet 2002, 3(1):53-64. 10.1038/nrg704, 11823791.
11. Shima A, Shimada A. Development of a possible nonmammalian test system for radiation-induced germ-cell mutagenesis using a fish, the Japanese medaka (Oryzias latipes). Proc Natl Acad Sci USA 1991, 88(6):2545-2549. 10.1073/pnas.88.6.2545, 51269, 2006189.
12. Hartwell LH, Weinert TA. Checkpoints: controls that ensure the order of cell cycle events. Science 1989, 246(4930):629-634. 10.1126/science.2683079, 2683079.
13. Zhou BB, Elledge SJ. The DNA damage response: putting checkpoints in perspective. Nature 2000, 408(6811):433-439. 10.1038/35044005, 11100718.
14. Lobrich M, Jeggo PA. The impact of a negligent G2/M checkpoint on genomic instability and cancer induction. Nat Rev Cancer 2007, 7(11):861-869. 10.1038/nrc2248, 17943134.
15. Lavin MF. Ataxia-telangiectasia: from a rare disorder to a paradigm for cell signalling and cancer. Nat Rev Mol Cell Biol 2008, 9(10):759-769. 10.1038/nrm2514, 18813293.
16. Cimprich KA, Cortez D. ATR: an essential regulator of genome integrity. Nat Rev Mol Cell Biol 2008, 9(8):616-627. 10.1038/nrm2450, 2663384, 18594563.
17. Shiloh Y. The ATM-mediated DNA-damage response: taking shape. Trends Biochem Sci 2006, 31(7):402-410. 10.1016/j.tibs.2006.05.004, 16774833.
18. Abraham RT. PI 3-kinase related kinases: 'big' players in stress-induced signaling pathways. DNA Repair (Amst) 2004, 3(8-9):883-887. 10.1016/j.dnarep.2004.04.002, 15279773.
19. Canman CE, Lim DS, Cimprich KA, Taya Y, Tamai K, Sakaguchi K, Appella E, Kastan MB, Siliciano JD. Activation of the ATM kinase by ionizing radiation and phosphorylation of p53. Science 1998, 281(5383):1677-1679. 10.1126/science.281.5383.1677, 9733515.
20. Mitani H, Kamei Y, Fukamachi S, Oda S, Sasaki T, Asakawa S, Todo T, Shimizu N. The medaka genome: why we need multiple fish models in vertebrate functional genomics. Genome Dyn 2006, 2:165-182. full_text, 18753778.
21. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin Chem 2003, 49(6 Pt 1):853-860. 10.1373/49.6.853, 12765979.
22. Erali M, Voelkerding KV, Wittwer CT. High resolution melting applications for clinical laboratory medicine. Exp Mol Pathol 2008, 85(1):50-58. 10.1016/j.yexmp.2008.03.012, 2606052, 18502416.
23. Herrmann MG, Durtschi JD, Bromley LK, Wittwer CT, Voelkerding KV. Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clin Chem 2006, 52(3):494-503. 10.1373/clinchem.2005.063438, 16423901.
24. Herrmann MG, Durtschi JD, Wittwer CT, Voelkerding KV. Expanded instrument comparison of amplicon DNA melting analysis for mutation scanning and genotyping. Clin Chem 2007, 53(8):1544-1548. 10.1373/clinchem.2007.088120, 17556647.
25. Gady AL, Hermans FW, Van de Wal MH, van Loo EN, Visser RG, Bachem CW. Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations. Plant Methods 2009, 5:13. 10.1186/1746-4811-5-13, 2763861, 19811648.
26. Reed GH, Wittwer CT. Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 2004, 50(10):1748-1754. 10.1373/clinchem.2003.029751, 15308590.
27. Brown EJ, Baltimore D. ATR disruption leads to chromosomal fragmentation and early embryonic lethality. Genes Dev 2000, 14(4):397-402. 316378, 10691732.
28. de Klein A, Muijtjens M, van Os R, Verhoeven Y, Smit B, Carr AM, Lehmann AR, Hoeijmakers JH. Targeted disruption of the cell-cycle checkpoint gene ATR leads to early embryonic lethality in mice. Curr Biol 2000, 10(8):479-482. 10.1016/S0960-9822(00)00447-4, 10801416.
29. Barlow C, Hirotsune S, Paylor R, Liyanage M, Eckhaus M, Collins F, Shiloh Y, Crawley JN, Ried T, Tagle D, et al. Atm-deficient mice: a paradigm of ataxia telangiectasia. Cell 1996, 86(1):159-171. 10.1016/S0092-8674(00)80086-0, 8689683.
30. Xu Y, Ashley T, Brainerd EE, Bronson RT, Meyn MS, Baltimore D. Targeted disruption of ATM leads to growth retardation, chromosomal fragmentation during meiosis, immune defects, and thymic lymphoma. Genes Dev 1996, 10(19):2411-2422. 10.1101/gad.10.19.2411, 8843194.
31. Elson A, Wang Y, Daugherty CJ, Morton CC, Zhou F, Campos-Torres J, Leder P. Pleiotropic defects in ataxia-telangiectasia protein-deficient mice. Proc Natl Acad Sci USA 1996, 93(23):13084-13089. 10.1073/pnas.93.23.13084, 24050, 8917548.
32. Saito D, Morinaga C, Aoki Y, Nakamura S, Mitani H, Furutani-Seiki M, Kondoh H, Tanaka M. Proliferation of germ cells during gonadal sex differentiation in medaka: Insights from germ cell-depleted mutant zenzai. Dev Biol 2007, 310(2):280-290. 10.1016/j.ydbio.2007.07.039, 17825277.
33. Longhese MP, Bonetti D, Guerini I, Manfrini N, Clerici M. DNA double-strand breaks in meiosis: checking their formation, processing and repair. DNA Repair (Amst) 2009, 8(9):1127-1138. 10.1016/j.dnarep.2009.04.005, 19464965.
34. Petronczki M, Siomos MF, Nasmyth K. Un menage a quatre: the molecular biology of chromosome segregation in meiosis. Cell 2003, 112(4):423-440. 10.1016/S0092-8674(03)00083-7, 12600308.
35. Keeney S, Giroux CN, Kleckner N. Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell 1997, 88(3):375-384. 10.1016/S0092-8674(00)81876-0, 9039264.
36. Terzoudi GI, Manola KN, Pantelias GE, Iliakis G. Checkpoint abrogation in G2 compromises repair of chromosomal breaks in ataxia telangiectasia cells. Cancer Res 2005, 65(24):11292-11296. 10.1158/0008-5472.CAN-05-2148, 16357135.
37. Hartwell LH, Kastan MB. Cell cycle control and cancer. Science 1994, 266(5192):1821-1828. 10.1126/science.7997877, 7997877.
38. Hamer G, Kal HB, Westphal CH, Ashley T, de Rooij DG. Ataxia telangiectasia mutated expression and activation in the testis. Biol Reprod 2004, 70(4):1206-1212. 10.1095/biolreprod.103.024950, 14681204.
39. Garcia V, Bruchet H, Camescasse D, Granier F, Bouchez D, Tissier A. AtATM is essential for meiosis and the somatic response to DNA damage in plants. Plant Cell 2003, 15(1):119-132. 10.1105/tpc.006577, 143473, 12509526.
40. Young DB, Jonnalagadda J, Gatei M, Jans DA, Meyn S, Khanna KK. Identification of domains of ataxia-telangiectasia mutated required for nuclear localization and chromatin association. J Biol Chem 2005, 280(30):27587-27594. 10.1074/jbc.M411689200, 15929992.
41. Lavin MF, Scott S, Gueven N, Kozlov S, Peng C, Chen P. Functional consequences of sequence alterations in the ATM gene. DNA Repair (Amst) 2004, 3(8-9):1197-1205. 10.1016/j.dnarep.2004.03.011, 15279808.
42. Meyn MS. Ataxia-telangiectasia, cancer and the pathobiology of the ATM gene. Clin Genet 1999, 55(5):289-304. 10.1034/j.1399-0004.1999.550501.x, 10422797.
43. Furutani-Seiki M, Sasado T, Morinaga C, Suwa H, Niwa K, Yoda H, Deguchi T, Hirose Y, Yasuoka A, Henrich T, et al. A systematic genome-wide screen for mutations affecting organogenesis in Medaka, Oryzias latipes. Mech Dev 2004, 121(7-8):647-658. 10.1016/j.mod.2004.04.016, 15210174.
44. Montgomery J, Wittwer CT, Palais R, Zhou L. Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis. Nat Protoc 2007, 2(1):59-66. 10.1038/nprot.2007.10, 17401339.
45. Palais RA, Liew MA, Wittwer CT. Quantitative heteroduplex analysis for single nucleotide polymorphism genotyping. Anal Biochem 2005, 346(1):167-175. 10.1016/j.ab.2005.08.010, 16188219.
46. Graham R, Liew M, Meadows C, Lyon E, Wittwer CT. Distinguishing different DNA heterozygotes by high-resolution melting. Clin Chem 2005, 51(7):1295-1298. 10.1373/clinchem.2005.051516, 15905310.
47. Kamei Y, Itou J, Oda S, Masui M, Kim JH, Ishikawa T, Yuba S, Kinoshita M, Mitani H, Todo T. Development of a convenient in vitro fertilization method using interspecific hybrids between Oryzias latipes and Oryzias curvinotus. Dev Growth Differ 2007, 49(9):721-730. 10.1111/j.1440-169X.2007.00966.x, 17983366.