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. 1996 Dec;144(4):1735–1745. doi: 10.1093/genetics/144.4.1735

Identification of Selected Gamma-Ray Induced Deficiencies in Zebrafish Using Multiplex Polymerase Chain Reaction

A Fritz 1, M Rozowski 1, C Walker 1, M Westerfield 1
PMCID: PMC1207723  PMID: 8978059

Abstract

The ease with which mutations can be generated in zebrafish makes this vertebrate an important resource for developmental genetics and genome studies. We have developed a PCR-based screening method that allows the efficient identification of gamma-ray induced deficiencies targeted to selected sequences. We describe three mutants characteristic of our findings and show that these mutations include deletions and translocations that can affect as much as 1% of the genome. These deficiencies provide a basis for analyzing the functions of cloned zebrafish genes using noncomplementation screens for point mutations induced by high-efficiency chemical mutagenesis.

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Selected References

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  1. Akimenko M. A., Ekker M., Wegner J., Lin W., Westerfield M. Combinatorial expression of three zebrafish genes related to distal-less: part of a homeobox gene code for the head. J Neurosci. 1994 Jun;14(6):3475–3486. doi: 10.1523/JNEUROSCI.14-06-03475.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Akimenko M. A., Johnson S. L., Westerfield M., Ekker M. Differential induction of four msx homeobox genes during fin development and regeneration in zebrafish. Development. 1995 Feb;121(2):347–357. doi: 10.1242/dev.121.2.347. [DOI] [PubMed] [Google Scholar]
  3. Batzer M. A., Tedeschi B., Fossett N. G., Tucker A., Kilroy G., Arbour P., Lee W. R. Spectra of molecular changes induced in DNA of Drosophila spermatozoa by 1-ethyl-1-nitrosourea and X-rays. Mutat Res. 1988 May;199(1):255–268. doi: 10.1016/0027-5107(88)90253-9. [DOI] [PubMed] [Google Scholar]
  4. Cattanach B. M., Burtenshaw M. D., Rasberry C., Evans E. P. Large deletions and other gross forms of chromosome imbalance compatible with viability and fertility in the mouse. Nat Genet. 1993 Jan;3(1):56–61. doi: 10.1038/ng0193-56. [DOI] [PubMed] [Google Scholar]
  5. Chakrabarti S., Streisinger G., Singer F., Walker C. Frequency of gamma-Ray Induced Specific Locus and Recessive Lethal Mutations in Mature Germ Cells of the Zebrafish, BRACHYDANIO RERIO. Genetics. 1983 Jan;103(1):109–123. doi: 10.1093/genetics/103.1.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chia W., Savakis C., Karp R., Pelham H., Ashburner M. Mutation of the Adh gene of Drosophila melanogaster containing an internal tandem duplication. J Mol Biol. 1985 Dec 20;186(4):679–688. doi: 10.1016/0022-2836(85)90388-2. [DOI] [PubMed] [Google Scholar]
  7. Driever W., Stemple D., Schier A., Solnica-Krezel L. Zebrafish: genetic tools for studying vertebrate development. Trends Genet. 1994 May;10(5):152–159. doi: 10.1016/0168-9525(94)90091-4. [DOI] [PubMed] [Google Scholar]
  8. Eeken J. C., de Jong A. W., Loos M., Vreeken C., Romeyn R., Pastink A., Lohman P. H. The nature of X-ray-induced mutations in mature sperm and spermatogonial cells of Drosophila melanogaster. Mutat Res. 1994 May 1;307(1):201–212. doi: 10.1016/0027-5107(94)90293-3. [DOI] [PubMed] [Google Scholar]
  9. Ekker M., Wegner J., Akimenko M. A., Westerfield M. Coordinate embryonic expression of three zebrafish engrailed genes. Development. 1992 Dec;116(4):1001–1010. doi: 10.1242/dev.116.4.1001. [DOI] [PubMed] [Google Scholar]
  10. Felsenfeld A. L., Walker C., Westerfield M., Kimmel C., Streisinger G. Mutations affecting skeletal muscle myofibril structure in the zebrafish. Development. 1990 Mar;108(3):443–459. doi: 10.1242/dev.108.3.443. [DOI] [PubMed] [Google Scholar]
  11. Fuscoe J. C., Zimmerman L. J., Fekete A., Setzer R. W., Rossiter B. J. Analysis of X-ray-induced HPRT mutations in CHO cells: insertion and deletions. Mutat Res. 1992 Oct;269(2):171–183. doi: 10.1016/0027-5107(92)90198-b. [DOI] [PubMed] [Google Scholar]
  12. Good P. J. A conserved family of elav-like genes in vertebrates. Proc Natl Acad Sci U S A. 1995 May 9;92(10):4557–4561. doi: 10.1073/pnas.92.10.4557. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gossen J. A., Martus H. J., Wei J. Y., Vijg J. Spontaneous and X-ray-induced deletion mutations in a LacZ plasmid-based transgenic mouse model. Mutat Res. 1995 Sep;331(1):89–97. doi: 10.1016/0027-5107(95)00055-n. [DOI] [PubMed] [Google Scholar]
  14. Grunwald D. J., Kimmel C. B., Westerfield M., Walker C., Streisinger G. A neural degeneration mutation that spares primary neurons in the zebrafish. Dev Biol. 1988 Mar;126(1):115–128. doi: 10.1016/0012-1606(88)90245-x. [DOI] [PubMed] [Google Scholar]
  15. Halpern M. E., Ho R. K., Walker C., Kimmel C. B. Induction of muscle pioneers and floor plate is distinguished by the zebrafish no tail mutation. Cell. 1993 Oct 8;75(1):99–111. [PubMed] [Google Scholar]
  16. Hatta K., Kimmel C. B., Ho R. K., Walker C. The cyclops mutation blocks specification of the floor plate of the zebrafish central nervous system. Nature. 1991 Mar 28;350(6316):339–341. doi: 10.1038/350339a0. [DOI] [PubMed] [Google Scholar]
  17. Johnson S. L., Gates M. A., Johnson M., Talbot W. S., Horne S., Baik K., Rude S., Wong J. R., Postlethwait J. H. Centromere-linkage analysis and consolidation of the zebrafish genetic map. Genetics. 1996 Apr;142(4):1277–1288. doi: 10.1093/genetics/142.4.1277. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Johnson S. L., Midson C. N., Ballinger E. W., Postlethwait J. H. Identification of RAPD primers that reveal extensive polymorphisms between laboratory strains of zebrafish. Genomics. 1994 Jan 1;19(1):152–156. doi: 10.1006/geno.1994.1026. [DOI] [PubMed] [Google Scholar]
  19. Kagawa Y., Yatagai F., Suzuki M., Kase Y., Kobayashi A., Hirano M., Kato T., Watanabe M., Hanaoka F. Analysis of mutations in the human HPRT gene induced by accelerated heavy-ion irradiation. J Radiat Res. 1995 Sep;36(3):185–195. doi: 10.1269/jrr.36.185. [DOI] [PubMed] [Google Scholar]
  20. Kelley M. R., Mims I. P., Farnet C. M., Dicharry S. A., Lee W. R. Molecular analysis of X-ray-induced alcohol dehydrogenase (ADH) null mutations in Drosophila melanogaster. Genetics. 1985 Feb;109(2):365–377. doi: 10.1093/genetics/109.2.365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kubota Y., Shimada A., Shima A. DNA alterations detected in the progeny of paternally irradiated Japanese medaka fish (Oryzias latipes). Proc Natl Acad Sci U S A. 1995 Jan 3;92(1):330–334. doi: 10.1073/pnas.92.1.330. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kubota Y., Shimada A., Shima A. Detection of gamma-ray-induced DNA damages in malformed dominant lethal embryos of the Japanese medaka (Oryzias latipes) using AP-PCR fingerprinting. Mutat Res. 1992 Dec;283(4):263–270. doi: 10.1016/0165-7992(92)90058-p. [DOI] [PubMed] [Google Scholar]
  23. Molven A., Hordvik I., Njølstad P. R., van Ghelue M., Fjose A. The zebrafish homeobox gene hox[zf-114]: primary structure, expression pattern and evolutionary aspects. Int J Dev Biol. 1992 Jun;36(2):229–237. [PubMed] [Google Scholar]
  24. Morris T., Masson W., Singleton B., Thacker J. Analysis of large deletions in the HPRT gene of primary human fibroblasts using the polymerase chain reaction. Somat Cell Mol Genet. 1993 Jan;19(1):9–19. doi: 10.1007/BF01233950. [DOI] [PubMed] [Google Scholar]
  25. Nelson S. L., Giver C. R., Grosovsky A. J. Spectrum of X-ray-induced mutations in the human hprt gene. Carcinogenesis. 1994 Mar;15(3):495–502. doi: 10.1093/carcin/15.3.495. [DOI] [PubMed] [Google Scholar]
  26. Nelson S. L., Jones I. M., Fuscoe J. C., Burkhart-Schultz K., Grosovsky A. J. Mapping the end points of large deletions affecting the hprt locus in human peripheral blood cells and cell lines. Radiat Res. 1995 Jan;141(1):2–10. [PubMed] [Google Scholar]
  27. Njølstad P. R., Molven A., Apold J., Fjose A. The zebrafish homeobox gene hox-2.2: transcription unit, potential regulatory regions and in situ localization of transcripts. EMBO J. 1990 Feb;9(2):515–524. doi: 10.1002/j.1460-2075.1990.tb08138.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Njølstad P. R., Molven A., Fjose A. A zebrafish homologue of the murine Hox-2.1 gene. FEBS Lett. 1988 Mar 28;230(1-2):25–30. doi: 10.1016/0014-5793(88)80634-3. [DOI] [PubMed] [Google Scholar]
  29. Park M. S., Hanks T., Jaberaboansari A., Chen D. J. Molecular analysis of gamma-ray-induced mutations at the hprt locus in primary human skin fibroblasts by multiplex polymerase chain reaction. Radiat Res. 1995 Jan;141(1):11–18. [PubMed] [Google Scholar]
  30. Pastink A., Schalet A. P., Vreeken C., Parádi E., Eeken J. C. The nature of radiation-induced mutations at the white locus of Drosophila melanogaster. Mutat Res. 1987 Mar;177(1):101–115. doi: 10.1016/0027-5107(87)90026-1. [DOI] [PubMed] [Google Scholar]
  31. Postlethwait J. H., Johnson S. L., Midson C. N., Talbot W. S., Gates M., Ballinger E. W., Africa D., Andrews R., Carl T., Eisen J. S. A genetic linkage map for the zebrafish. Science. 1994 Apr 29;264(5159):699–703. doi: 10.1126/science.8171321. [DOI] [PubMed] [Google Scholar]
  32. Puck T. T., Harvey W. F. Gamma-ray mutagenesis measurement in mammalian cells. Mutat Res. 1995 Jul;329(2):173–181. doi: 10.1016/0027-5107(95)00028-h. [DOI] [PubMed] [Google Scholar]
  33. Qiao T., Maddox B. K., Erickson H. P. A novel alternative splice domain in zebrafish tenascin-C. Gene. 1995 Apr 24;156(2):307–308. doi: 10.1016/0378-1119(95)00039-9. [DOI] [PubMed] [Google Scholar]
  34. Rancourt D. E., Tsuzuki T., Capecchi M. R. Genetic interaction between hoxb-5 and hoxb-6 is revealed by nonallelic noncomplementation. Genes Dev. 1995 Jan 1;9(1):108–122. doi: 10.1101/gad.9.1.108. [DOI] [PubMed] [Google Scholar]
  35. Riley B. B., Grunwald D. J. Efficient induction of point mutations allowing recovery of specific locus mutations in zebrafish. Proc Natl Acad Sci U S A. 1995 Jun 20;92(13):5997–6001. doi: 10.1073/pnas.92.13.5997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Rinchik E. M., Bangham J. W., Hunsicker P. R., Cacheiro N. L., Kwon B. S., Jackson I. J., Russell L. B. Genetic and molecular analysis of chlorambucil-induced germ-line mutations in the mouse. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1416–1420. doi: 10.1073/pnas.87.4.1416. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Rinchik E. M. Chemical mutagenesis and fine-structure functional analysis of the mouse genome. Trends Genet. 1991 Jan;7(1):15–21. doi: 10.1016/0168-9525(91)90016-j. [DOI] [PubMed] [Google Scholar]
  38. Rossiter B. J., Fuscoe J. C., Muzny D. M., Fox M., Caskey C. T. The Chinese hamster HPRT gene: restriction map, sequence analysis, and multiplex PCR deletion screen. Genomics. 1991 Feb;9(2):247–256. doi: 10.1016/0888-7543(91)90249-e. [DOI] [PubMed] [Google Scholar]
  39. Schwartz J. L., Rotmensch J., Sun J., An J., Xu Z., Yu Y., Hsie A. W. Multiplex polymerase chain reaction-based deletion analysis of spontaneous, gamma ray- and alpha-induced hprt mutants of CHO-K1 cells. Mutagenesis. 1994 Nov;9(6):537–540. doi: 10.1093/mutage/9.6.537. [DOI] [PubMed] [Google Scholar]
  40. Shima A., Shimada A. The Japanese medaka, Oryzias latipes, as a new model organism for studying environmental germ-cell mutagenesis. Environ Health Perspect. 1994 Dec;102 (Suppl 12):33–35. doi: 10.1289/ehp.94102s1233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Shukla P. T., Sankaranarayanan K., Sobels F. H. Is there a proportionality between the spontaneous and the X-ray-induction rates of mutations? Experiments with mutations at 13 X-chromosome loci in Drosophila melanogaster. Mutat Res. 1979 Jul;61(2):229–248. doi: 10.1016/0027-5107(79)90130-1. [DOI] [PubMed] [Google Scholar]
  42. Solnica-Krezel L., Schier A. F., Driever W. Efficient recovery of ENU-induced mutations from the zebrafish germline. Genetics. 1994 Apr;136(4):1401–1420. doi: 10.1093/genetics/136.4.1401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Stachel S. E., Grunwald D. J., Myers P. Z. Lithium perturbation and goosecoid expression identify a dorsal specification pathway in the pregastrula zebrafish. Development. 1993 Apr;117(4):1261–1274. doi: 10.1242/dev.117.4.1261. [DOI] [PubMed] [Google Scholar]
  44. Streisinger G., Walker C., Dower N., Knauber D., Singer F. Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature. 1981 May 28;291(5813):293–296. doi: 10.1038/291293a0. [DOI] [PubMed] [Google Scholar]
  45. Strähle U., Blader P., Henrique D., Ingham P. W. Axial, a zebrafish gene expressed along the developing body axis, shows altered expression in cyclops mutant embryos. Genes Dev. 1993 Jul;7(7B):1436–1446. doi: 10.1101/gad.7.7b.1436. [DOI] [PubMed] [Google Scholar]
  46. Stuart G. W., McMurray J. V., Westerfield M. Replication, integration and stable germ-line transmission of foreign sequences injected into early zebrafish embryos. Development. 1988 Jun;103(2):403–412. doi: 10.1242/dev.103.2.403. [DOI] [PubMed] [Google Scholar]
  47. Tachibana A., Ohbayashi T., Takebe H., Tatsumi K. Molecular changes in UV-induced and gamma-ray-induced mutations in human lymphoblastoid cells. Mutat Res. 1990 Jun;230(2):159–166. doi: 10.1016/0027-5107(90)90053-7. [DOI] [PubMed] [Google Scholar]
  48. Talbot W. S., Trevarrow B., Halpern M. E., Melby A. E., Farr G., Postlethwait J. H., Jowett T., Kimmel C. B., Kimelman D. A homeobox gene essential for zebrafish notochord development. Nature. 1995 Nov 9;378(6553):150–157. doi: 10.1038/378150a0. [DOI] [PubMed] [Google Scholar]
  49. Tease C., Fisher G. Cytogenetic and genetic studies of radiation-induced chromosome damage in mouse oocytes. I. Numerical and structural chromosome anomalies in metaphase II oocytes, pre- and post-implantation embryos. Mutat Res. 1996 Jan 17;349(1):145–153. doi: 10.1016/0027-5107(95)00182-4. [DOI] [PubMed] [Google Scholar]
  50. Tease C., Fisher G. Cytogenetic and genetic studies of radiation-induced chromosome damage in mouse oocytes. II. Induced chromosome loss and dominant visible mutations. Mutat Res. 1996 Jan 17;349(1):155–162. doi: 10.1016/0027-5107(95)00183-2. [DOI] [PubMed] [Google Scholar]
  51. Tongiorgi E., Bernhardt R. R., Zinn K., Schachner M. Tenascin-C mRNA is expressed in cranial neural crest cells, in some placodal derivatives, and in discrete domains of the embryonic zebrafish brain. J Neurobiol. 1995 Nov;28(3):391–407. doi: 10.1002/neu.480280311. [DOI] [PubMed] [Google Scholar]
  52. Walker C., Streisinger G. Induction of Mutations by gamma-Rays in Pregonial Germ Cells of Zebrafish Embryos. Genetics. 1983 Jan;103(1):125–136. doi: 10.1093/genetics/103.1.125. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Westerfield M., Liu D. W., Kimmel C. B., Walker C. Pathfinding and synapse formation in a zebrafish mutant lacking functional acetylcholine receptors. Neuron. 1990 Jun;4(6):867–874. doi: 10.1016/0896-6273(90)90139-7. [DOI] [PubMed] [Google Scholar]
  54. Yu Y. J., Xu Z., Gibbs R. A., Hsie A. W. Polymerase chain reaction-based comprehensive procedure for the analysis of the mutation spectrum at the hypoxanthine-guanine phosphoribosyltransferase locus in Chinese hamster cells. Environ Mol Mutagen. 1992;19(4):267–273. doi: 10.1002/em.2850190402. [DOI] [PubMed] [Google Scholar]
  55. Zu Z., Yu Y., Gibbs R. A., Caskey C. T., Hsie A. W. Multiplex DNA amplification and solid-phase direct sequencing for mutation analysis at the hprt locus in Chinese hamster cells. Mutat Res. 1993 Aug;288(2):237–248. doi: 10.1016/0027-5107(93)90090-3. [DOI] [PubMed] [Google Scholar]
  56. van Buul P. P., Léonard A., Goudzwaard J. H. Dose-effect relationship for X-ray-induced reciprocal translocations in mouse spermatogonia following pretreatment with 3-aminobenzamide. Mutat Res. 1990 Oct;232(2):273–280. doi: 10.1016/0027-5107(90)90134-p. [DOI] [PubMed] [Google Scholar]

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