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Даніо – нова модельна система експериментальної біології

Корж В., Кондричин І., Віната Ц.

Оригінальна работа 




Поява геноміки та її використання у поєднанні з біоіміджингом з високою роздільною здатністю для вивчення механізмів розвитку тварин забезпечують науковців інформацією про набори генів та їх регуляцію під час розвитку. Це призвело до виявлення основного набору факторів транскрипції, що беруть участь у розвитку безхребетних та хребетних тварин. Цей підхід був особливо корисним завдяки широкому використанню у цих дослідженнях напівпрозорих ембріонів даніо та інших кісткових риб, використовуючи які як модельні системи розвитку хребетних тварин можна аналізувати навіть на рівні однієї клітини як різні процеси розвитку відбуваються in vivo.

Ключові слова: геноміка розвитку, трансгенез, Tol2 транспозон, біоімаджінг, латеральна лінія, Zic3

Цитологія і генетика 2018, том 52, № 6, C. 18-29

  • Міжнародний інститут молекулярної і клітинної біології, Варшава, Польща
  • RIKEN Центр Дослідження Динаміки Біосистем, Кобе, Японія
  • Інститут Макса Планка до Вивчення серця і легень, Бад Нойхайм, Німеччина

E-mail: vkorzh iimcb.gov.pl, igor.kondrychyn riken.jp, cwinata iimcb.gov.pl

Корж В., Кондричин І., Віната Ц. Даніо – нова модельна система експериментальної біології, Цитологія і генетика., 2018, том 52, № 6, C. 18-29.

В "Cytology and Genetics". Якщо тільки можливо, цитуйте статтю по нашій англомовній версії:
V. Korzh, I. Kondrychyn, C. Winata The Zebrafish as a New Model System for Experimental Biology, Cytol Genet., 2018, vol. 52, no. 6, pp. 406–415
DOI: 10.3103/S009545271806004X


Посилання

1. Korzh, V. and Bregestovski, P., Elie Metchnikoff: Father of phagocytosis theory and pioneer of experiments in vivo, Cytol. Genet., 2016, vol. 50, no. 2, pp. 143–150.

2. Korzh, V., Genetic control of early neuronal development in vertebrates, Curr. Opin. Neurobiol., 1994, vol. 4, no. 1, pp. 21–28. org/ doi 10.1016/0959-4388(94)90027-2

3. Kimmel, C.B., Ballard, W.W., Kimmel, S.R., Ullmann, B., and Schilling, T.F., Stages of embryonic development of the zebrafish, Dev. Dynam., 1995, vol. 203, no. 3, pp. 253–310. doi 10.1002/aja.1002030302

4. Westerfield, M., A Guide for the Laboratory Use of Zebrafish (Brachydanio rerio), Eugene OR: Univ. of Oregon Press, 1995.

5. Barriuso, J., Nagaraju, R., and Hurlstone, A., Zebrafish: a new companion for translational research in oncology, Clin. Cancer Res., 2015, vol. 21, no. 5, pp. 969–975. doi 10.1158/1078-0432.CCR-14-2921

6. Patten, S.A., Armstrong, G.A., Lissouba, A., Kabashi, E., Parker, J.A., and Drapeau, P., Fishing for causes and cures of motor neuron disorders, Dis. Model. Mech., 2014, vol. 7, no. 7, pp. 799–809. doi 10.1242/ dmm.015719

7. Li, M., Zhao, L., Page-McCaw, P.S., and Chen, W., Zebrafish Genome Engineering Using the CRISPRCas9 System, Trends Genet., 2016, vol. 32, no. 12. doi 10.1016/j.tig.2016.10.005

8. Peterson, R.T., Zebrafish as tools for drug discovery, Nat. Rev. Drug. Discov., 2015, vol. 14, no. 10, pp. 721–731. doi 10.1038/nrd4627

9. Yan, H., The C., Sreejith S., Zhu L.L., Kwok A., Ma X., Nguyen K.T., Korzh V., Zhao Y. Functional mechanized mesoporous silica nano-particles for controlled drug release in vivo, Angew. Chem. Int., vol. 51, no. 33, pp. 8373–8377. doi 10.1002/anie.201203993

10. Aanes, H., Winata, C.L., Lin, C.H., Chen, J.P., Srinivasan, K.G., Lee, S.G., Lim, A.Y., Hajan, H.S., Collas, P., Bourque, G., Gong, Z., Korzh, V., Alestrom, P., and Mathavan, S., Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition, Genome Res., 2011, vol. 21, no. 8, pp. 1328–1338. doi 10.1101/gr.116012.110

11. Winata, C.L., Kondrychyn, I., Kumar, V., Srinivasan, K.G., Orlov, Yu., Ravishankar, A., Prabhakar, S., Stanton, L., Korzh, V., and Mathavan, S., Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish, PLoS Genet., 2013, vol. 9, no. 10. e1003852. doi 10.1371/journal.pgen.1003852

12. Winata, C.L., Kondrychyn, I., and Korzh, V., Changing faces of transcriptional regulation by Zic3, Curr. Genom., 2015, vol. 16, no. 2, pp. 117–27. 10.2174/ 1389202916666150205124519

13. Mikut, R., Dickmeis, T., Driever, W., Geurts, P., Hamprecht, F.A., Kausler, B.X., Ledesma-Carbayo, M.J., Maree, R., Mikula, K., Pantazis, P., Ronneberger, O., Santos, A., Stotzka, R., Strahle, U., and Peyrieras, N., Automated processing of zebrafish imaging data: a survey, Zebra Fish, 2013, vol. 10, no. 3, pp. 401–421. doi 10.1089/zeb.2013.0886

14. Fraser, P., Transcriptional control thrown for a loop, Curr. Opin. Genet. Dev., 2006, vol. 1, no. 5, pp. 490–495.

15. Weipoltshammer, K. and Schofer, C., Morphology of nuclear transcription, Histochem., Cell Biol., 2016, vol. 145, no. 4, pp. 343–358. doi 10.1007/s00418-016-1412-0

16. Howe, K., Clark, M.D., Torroja, C.F., Torrance, J., Berthelot, C., Muffato, M., Collins, J.E., Humphray, S., McLaren, K., Matthews, L., McLaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J.C., Koch, R., Rauch, G.J., White, S., Chow, W., Kilian, B., Quintais, L.T., Guerra-Assuncao, J.A., Zhou, Y., Gu, Y., Yen, J., Vogel, J.H., Eyre, T., Redmond, S., Banerjee, R., Chi, J., Fu, B., Langley, E., Maguire, S.F., Laird, G.K., Lloyd, D., Kenyon, E., Donaldson, S., Sehra, H., Almeida-King, J., Loveland, J., Trevanion, S., Jones, M., Quail, M., Willey, D., Hunt, A., Burton, J., Sims, S., McLay, K., Plumb, B., Davis, J., Clee, C., Oliver, K., Clark, R., Riddle, C., Elliot, D., Threadgold, G., Harden, G., Ware, D., Begum, S., Mortimore, B., Kerry, G., Heath, P., Phillimore, B., Tracey, A., Corby, N., Dunn, M., Johnson, C., Wood, J., Clark, S., Pelan, S., Griffiths, G., Smith, M., Glithero, R., Howden, P., Barker, N., Lloyd, C., Stevens, C., Harley, J., Holt, K., Panagiotidis, G., Lovell, J., Beasley, H., Henderson, C., Gordon, D., Auger, K., Wright, D., Collins, J., Raisen, C., Dyer, L., Leung, K., Robertson, L., Ambridge, K., Leongamornlert, D., McGuire, S., Gilderthorp, R., Griffiths, C., Manthravadi, D., Nichol., S., Barker, G., Whitehead, S., Kay, M., Brown, J., Murnane, C., Gray, E., Humphries, M., Sycamore, N., Barker, D., Saunders, D., Wallis, J., Babbage, A., Hammond, S., Mashreghi-Mohammadi, M., Barr, L., Martin, S., Wray, P., Ellington, A., Matthews, N., Ellwood, M., Woodmansey, R., Clark, G., Cooper, J., Tromans, A., Grafham, D., Skuce, C., Pandian, R., Andrews, R., Harrison, E., Kimberley, A., Garnett, J., Fosker, N., Hall, R., Garner, P., Kelly, D., Bird, C., Palmer, S., Gehring, I., Berger, A., Dooley, C.M., Ersan-Urun, Z., Eser, C., Geiger, H., Geisler, M., Karotki, L., Kirn, A., Konantz, J., Konantz, M., Oberlander, M., Rudolph-Geiger, S., Teucke, M., Lanz, C., Raddatz, G., Osoegawa, K., Zhu, B., Rapp, A., Widaa, S., Langford, C., Yang, F., Schuster, S.C., Carter, N.P., Harrow, J., Ning, Z., Herrero, J., Searle, S.M., Enright, A., Geisler, R., Plasterk, R.H., Lee, C., Westerfield, M., de Jong, P.J., Zon, L.I., Postlethwait, J.H., Nusslein-Volhard, C., Hubbard, T.J., Roest Crollius, H., Rogers, J., and Stemple, D.L., The zebrafish reference genome sequence and its relationship to the human genome, Nature, 2013, vol. 496, no. 7446, pp. 498–503. doi 10.1038/nature12111

17. Kettleborough, R.N., Busch-Nentwich, E.M., Harvey, S.A., Dooley, C.M., de Bruijn, E., van Eeden, F., Sealy, I., White, R.J., Herd, C., Nijman, I.J., Fenyes, F., Mehroke, S., Scahill, C., Gibbons, R., Wali, N., Carruthers, S., Hall, A., Yen, J., Cuppen, E., and Stemple, D.L., A systematic genome-wide analysis of zebrafish protein-coding gene function, Nature, 2013, vol. 496, pp. 494–497.

18. Brenner, S., Elgar, G., Sandford, R., Macrae, A., Venkatesh, B., and Aparicio, S., Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome, Nature, 1993, vol. 366, no. 6452, pp. 265–268. doi 10.1038/366265a0

19. Venkatesh, B., Lee, A., Ravi, V., Lian, M., Maurya, A., Swann, J., Ohta, Y., Flajnik, M., Sutoh, Y., Kasahara, M., Hoon, S., Gangu, V., Roy, S., Irimia, M., Korzh, V., Kondrychyn, I., Tay, B.T., Tohari, S., Lim, S., Kong, K., Ho, S., Lorente-Galdos, B., Qui, J., Marques-Bonet, T., Raney, B., Ingham, P., Tay, A., Hillier, L., Minx, P., Boehm, T., Wilson, R., Brenner, S., and Warren, W., Elephant shark genome provides insights into gnathostome evolution, Nature, 2014, vol. 505, pp. 174–179.

20. Mathavan, S., Lee, S.G., Mak, A., Miller, L.D., Murthy, K.R., Govindarajan, K.R., Tong, Y., Wu, Y.L., Lam, S.H., Yang, H., Ruan, Y., Korzh, V., Gong, Z., Liu, E.T., and Lufkin, T., Transcriptome analysis of zebrafish embryogenesis using microarrays, PLoS Genet., 2005, vol. 1, no. 2, pp. 260–276. doi 10.1371/ journal.pgen.0010029

21. Harvey, S.A., Sealy, I., Kettleborough, R., Fenyes, F., White, R., Stemple, D., and Smith, J.C., Identification of the zebrafish maternal and paternal transcriptomes, Development, 2013, vol. 140, no. 13, pp. 2703–2710. doi 10.1242/dev.095091

22. Armant, O., Marz, M., Schmidt, R., Ferg, M., Diotel, N., Ertzer, R., Bryne, J.C., Yang, L., Baader, I., Reischl, M., Legradi, J., Mikut, R., Stemple, D., van IJcken, W., van der Sloot, A., Lenhard, B., Strahle, U., and Rastegar, S., Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos, Dev Biol., 2013, vol. 380, no. 2, pp. 351–362. doi 10.1016/j.ydbio.2013.05.006

23. Thisse, B. and Thisse, C., Fast release clones: a high throughput expression analysis, ZFIN direct data submission, 2004. http://zfin.org

24. Seth, A., Stemple, D.L., and Barroso, I., The emerging use of zebrafish to model metabolic disease, Dis. Model Mech., 2013, vol. 6, no. 5, pp. 1080–1088. doi 10.1242/dmm.011346

25. Tan, H., Onichtchouk, D., and Winata, C., DANIOCODE: toward an encyclopedia of DNA elements in zebrafish, Zebrafish, vol. 13, no. 1, pp. 54–60. doi 10.1089/zeb.2015.1179

26. Birnbaum, R.Y., Clowney, E.J., Agamy, O., Kim, M.J., Zhao, J., Yamanaka, T., Pappalardo, Z., Clar-ke, S.L., Wenger, A.M., Nguyen, L., Gurrieri, F., Everman, D.B., Schwartz, C.E., Birk, O.S., Beje-rano, G., Lomvardas, S., and Ahituv, N., Coding exons function as tissue-specific enhancers of nearby genes, Genome Res., 2012, vol. 22, no. 6, pp. 1059–1068. doi 10.1101/gr.133546.111

27. Gehrig, J., Reischl, M., Kalmar, E., Ferg, M., Hadzhiev, Y., Zaucker, A., Song, C., Schindler, S., Liebel, U., and Muller, F., Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos, Nat. Methods, 2009, vol. 6, no. 12, pp. 911–916. doi 10.1038/nmeth.1396

28. Gebbi, M., Ferrero, G.B., Pilia, G., Bassi, M.T., Aylsworth, A., Penman-Splitt, M., Bird, L.M., Bamforth, J.S., Burn, J., Schlessinger, D., Nelson, D.L., and Casey, B., X-linked situs abnormalities result from mutations in ZIC3, Nat. Genet., 1997, vol. 17, no. 3, pp. 305–308. doi 10.1038/ng1197-305

29. Ishiguro, A., Inoue, T., Mikoshiba, K., and Aruga, J., Molecular properties of Zic4 and Zic5 proteins: functional diversity within Zic family, Biochem. Biophys. Res. Commun., 2004, vol. 324, no. 1, pp. 302–307. doi 10.1016/j.bbrc.2004.09.052

30. Ware, S.M., Peng, J., Zhu, L., Fernbach, S., Colicos, S., Casey, B., Towbin, J., and Belmont, J.W., Identification and functional analysis of ZIC3 mutations in heterotaxy and related congenital heart defects, Am. J. Hum. Genet., 2004, vol. 74, no. 1, pp. 93–105. doi 10.1086/380998

31. Cowan, J., Tariq, M., and Ware, S.M., Genetic and functional analyses of ZIC3 variants in congenital heart disease, Hum. Mut., 2014, vol. 35, no. 1, pp. 66–75. doi 10.1002/humu.22457

32. Aruga, J., Yokota, N., Hashimoto, M., Furuichi, T., Fukuda, M., and Mikoshiba, K., A novel zinc finger protein, zic, is involved in neurogenesis, especially in the cell lineage of cerebellar granule cells, J. Neurochem., 1994, vol. 63, no. 5, pp. 1880–1890.

33. Logan, C.Y. and Nusse, R., The Wnt signaling pathway in development and disease, Ann. Rev. Cell Dev. Biol., 2004, vol. 20, pp. 781–810. doi 10.1146/annurev.cellbio.20.010403.113126

34. Nonaka, S., Tanaka, Y., Okada, Y., Takeda, S., Harada, A., Kanai, Y., Kido, M., and Hirokawa, N., Randomization of left-right asymmetry due to loss of nodal cilia generating leftward flow of extraembryonic fluid in mice lacking KIF3B motor protein, Cell, 1998, vol. 95, no. 6, pp. 829–837.

35. Tanaka, Y., Okada, Y., and Hirokawa, N., FGF-induced vesicular release of Sonic hedgehog and retinoic acid in leftward nodal flow is critical for left-right determination, Nature, 2005, vol. 435, no. 7039, pp. 172–177. doi 10.1038/nature03494

36. Essner, J.J., Amack, J.D., Nyholm, M.K., Harris, E.B., and Yost, H.J., Kupffer’s vesicle is a ciliated organ of asymmetry in the zebrafish embryo that initiates left-right development of the brain, heart and gut, Development, 2005, vol. 13, no. 6, pp. 1247–1260. doi 10.1242/dev.01663

37. Sampath, K., Rubinstein, A.L., Cheng, A.M., Liang, J.O., Fekany, K., Solnica-Krezel, L., Korzh, V., Halpern, M.E., and Wright, C.V., Induction of the zebrafish ventral brain and floor plate requires cyclops/nodal signaling, Nature, 1998, vol. 395, no. 6698, pp. 185–189. doi 10.1038/26020

38. Yu, X., Ng, C.P., Habacher, H., and Roy, S., Foxj1 transcription factors are master regulators of the motile ciliogenic program, Nat. Genet., 2008, vol. 40, no. 12, pp. 1445–1453. doi 10.1038/ng.263

39. Aruga, J., The role of Zic genes in neural development, Mol. Cell. Neurosci., 2004, vol. 26, no. 2, pp. 205–221.

40. Grinblat, Y. and Sive, H., Zic gene expression marks anteroposterior pattern in the presumptive neurectoderm of the zebrafish gastrula, Dev. Dyn., 2001, vol. 222, no. 1, pp. 688–693. doi 10.1002/dvdy.1221

41. Kondrychyn, I., Teh, C., Sin, M., and Korzh, V., Stretching morphogenesis of the roof plate during coordinated formation of the central canal, PLoS One, 2013, vol. 8, no. 2. e56219. doi 10.1371/journal.pone.0056219

42. Wan, H., He, J., Ju, B., Yan, T., Lam, T.J., and Gong, Z., Generation of two-color transgenic zebrafish using the green and red fluorescent protein reporter genes gfp and rfp, Mar. Biotechnol., 2002, vol. 4, no. 2, pp. 146–154. doi 10.1007/s10126-001-0085-3

43. Korzh, V. and Wohland, T., Analysis of single molecules in vivo or… why a small fish is better than an empty dish. Ontogenesis, Russ. J. Dev. Biol., 2012, vol. 43, no. 2, pp. 83–93.

44. Teh, C., Sun, G., Shen, H.Y., Korzh, V., and Wohland, T., Modulating the expression level of secreted Wnt3 influences cerebellum development in zebrafish transgenics, Development, 2015, vol. 142, no. 21, pp. 3721–3733. doi 10.1242/dev.127589

45. Keller, P.J., Schmidt, A.D., Wittbrodt, J., and Stelzer, E.H., Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy, Science, 2008, vol. 322, no. 5904, pp. 1065–1069. doi 10.1126/science.1162493

46. Long, Q., Meng, A., Wang, H., Jessen, J.R., Farrell, M.J., and Lin, S., GATA-1 expression pattern can be recapitulated in living transgenic zebrafish using GFP reporter gene, Development. 1997, vol. 124, no. 20, pp. 4105–4111.

47. Parinov, S., Kondrichin, I., Korzh, V., and Emelya-nov, A., Tol2 transposon-mediated enhancer trap to identify developmentally regulated zebrafish genes in vivo, Dev. Dynam., 2004, vol. 231, no. 2, pp. 449–459. doi 10.1002/dvdy.20157

48. Kawakami, K., Takeda, H., Kawakami, N., Kobayashi, M., Matsuda, N., and Mishina, M., A transposon-mediated gene trap approach identifies developmentally regulated genes in zebrafish, Dev. Cell, 2004, vol. 7, no. 1, pp. 133–144. doi 10.1016/j.devcel.2004.06.005

49. Emelyanov, A., Gao, Y., Naqvi, N.I., and Parinov, S., Trans-kingdom transposition of the maize dissociation element, Genetics, 2006, vol. 174, no. 3, pp. 1095–1104. org/ doi 10.1534/genetics.106.061184

50. Ivics, Z., Hackett, P.B., Plasterk, R.H., and Izsvak, Z., Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its trans-position in human cells, Cell, 1997, vol. 91, no. 4, pp. 501–510.

51. Kondrychyn, I., Garcia-Lecea, M., Emelyanov, A., Parinov, S., and Korzh, V., Genome-wide analysis of Tol2 transposon reintegration in zebrafish, BMC Genomics, 2009, vol. 10, pp. 418. doi 10.1186/1471-2164-10-418

52. Kondrychyn, I., Teh, C., Garcia-Lecea, M., Guan, Y., Kang, A., and Korzh, V., Zebrafish Enhancer TRAP transgenic line database ZETRAP 2.0, Zebrafish, 2011, vol. 8, no. 4, pp. 181–182. doi 10.1089/zeb.2011.0718

53. Garcia-Lecea, M., Kondrychyn, I., Fong, S.H., Ye, Z.-R., and Korzh, V., In vivo analysis of choroid plexus morphogenesis in zebrafish, PLoS One, 2008, vol. 3, no. 9. e3090. doi 10.1371/journal.pone.0003090.53

54. Sivasubbu, S., Balciunas, D., Amsterdam, A., and Ekker, S.C., Insertional mutagenesis strategies in zebrafish, Genome Biol., 2007, vol. 8, suppl. 1, p. S9. doi 10.1186/gb-2007-8-s1-s9

55. Go, W., Bessarab, D., and Korzh, V., atp2b1a regulates Ca(2+) export during differentiation and regeneration of mechanosensory hair cells in zebrafish, Cell Calcium, 2010, vol. 48, no. 5, pp. 302–313. doi 10.1016/ j.ceca.2010.09.012

56. Ghysen, A., Dambly-Chaudiere, C., and Raible, D., Making sense of zebrafish neural development in the Minervois, Neural. Dev., 2007, vol. 2, no. 1, p. 15. doi 10.1186/1749-8104-2-15

57. Gomez-Skarmeta, J.L., Lenhard, B., and Becker, T.S., New technologies, new findings, and new concepts in the study of vertebrate cis-regulatory sequences, Dev. Dyn., 2006, vol. 235, no. 4, pp. 870–885. doi 10.1002/dvdy.20659

58. Korzh, V., Transposons as tools for enhancer-trap screens in vertebrates, Genome Biol., 2007, vol. 8, suppl. 1, p. S8. doi 10.1186/gb-2007-8-s1-s8

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