The duplicated retinol-binding protein 7 (rbp7) genes are differentially transcribed in embryos and adult zebrafish (Danio rerio)

Gene Expression Patterns

Volumn 10, Issue 4-5, 2010, Pages 167-176

  Belliveau, Daniel J ^a   Venkatachalam, Ananda B ^a   Thisse, Christine ^b   Thisse, Bernard ^b   Ma, Hui ^b   Wright, Jonathan M ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b UNIVERSITY OF VIRGINIA HEALTH SYSTEM   (United States)

Author keywords

Conserved gene synteny; Duplicated genes; Gene phylogeny; Gene regulation; MRNA distribution; Radiation hybrid mapping; Rbp7; Teleost fishes; Whole genome duplication

Indexed keywords

DNA; RETINOL BINDING PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; GENE DUPLICATION; GENETICS; IN SITU HYBRIDIZATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRENATAL DEVELOPMENT; SEQUENCE HOMOLOGY; ZEBRA FISH;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; DNA; GENE DUPLICATION; IN SITU HYBRIDIZATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; RETINOL-BINDING PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; ZEBRAFISH;

EID: 77956637035     PISSN: 1567133X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gep.2010.04.003     Document Type: Article

References (37)

1. Bernlohr, D.A., Simpson, M.A., Hertzel, A.V., Banaszak, L.J., 1997. Intracellular lipidbinding proteins and their genes. Annu. Rev. Nutr. 17, 277-303.
2. Breathnach, R., Chambon, P., 1981. Organization and expression of eukaryotic split genes coding for proteins. Annu. Rev. Biochem. 50, 349-383.
3. Bustin, S.A., Benes, V., Nolan, T., Pfaffl, M.W., 2005. Quantitative real-time RT-PCR - a perspective. J. Mol. Endocrinol. 34, 597-601.
4. Cameron, M.C., Denovan-Wright, E.M., Sharma, M.K., Wright, J.M., 2002. Cellular retinol-binding protein type II (CRBPII) in adult zebrafish (Danio rerio). Eur. J. Biochem. 269, 4685-4692.
5. Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein, M., Werner, T., 2005. MatInspector and beyond: Promoter analysis based on transcription factor binding sites. Bioinformatics 21, 2933-2942.
6. Essner, J.J., Amack, J.D., Nyholm, M.K., Harris, E.B., Yost, H.J., 2005. 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 132, 1247-1260.
7. Folli, C., Calderone, V., Ramazzina, I., Zanotti, G., Berni, R., 2002. Ligand binding and structural analysis of a human putative cellular retinol-binding protein. J. Biol. Chem. 277, 41970-41977.
8. Force, A., Lynch, M., Pickett, F.B., Amores, A., Yan, Y.L., Postlethwait, J., 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531-1545.
9. Gates, M.A., Kim, L., Egan, E.S., Cardozo, T., Sirotkin, H.I., Dougan, S.T., Lashkari, D., Abagyan, R., Schier, A.F., Talbot, W.S., 1999. A genetic linkage map of zebrafish: Comparative analysis and localization of genes and expressed sequences. Genome Res. 9, 334-347.
10. Hukriede, N.A., Joly, L., Tsang, M., Miles, J., Tellis, P., Epstein, J.A., Barbazuk, W.B., Li, F.N., Paw, B., Postlethwait, J.H., Hudson, T.J., Zon, L.I., McPherson, J.D., Chevrette, M., Dawid, I.B., Johnson, S.L., Ekker, M., 1999. Radiation hybrid mapping of the zebrafish genome. Proc. Natl. Acad. Sci. USA 96, 9745-9750.
11. Hurley, I.A., Mueller, R.L., Dunn, K.A., Schmidt, E.J., Friedman, M., Ho, R.K., Prince, V.E., Yang, Z., Thomas, M.G., Coates, M.I., 2007. A new time-scale for ray-finned fish evolution. Proc. R. Soc. B. 274, 489-498.
12. Karanth, S., Denovan-Wright, E.M., Thisse, C., Thisse, B., Wright, J.M., 2008. The evolutionary relationship between the duplicated copies of the zebrafish fabp11 gene and the tetrapod FABP4, FABP5, FABP8 and FABP9 genes. FEBS J. 275, 3031-3040.
13. Karanth, S., Lall, S.P., Denovan-Wright, E.M., Wright, J.M., 2009a. Differential transcriptional modulation of duplicated fatty acid-binding protein genes by dietary fatty acids in zebrafish (Danio rerio): Evidence for subfunctionalization or neofunctionalization of duplicated genes. BMC Evol. Biol. 9, 219.
14. Karanth, S., Denovan-Wright, E.M., Thisse, C., THisse, B., Wright, J.M., 2009b. Tandem duplication and subsequent divergence of the tissue-specific distribution of fabp1b.1 and fabp1b.2 transcripts in zebrafish (Danio rerio). Genome 52, 985-992.
15. Kimmel, C.B., Ballard, W.W., Kimmel, S.R., Ullman, B., Schilling, T.F., 1995. Stages of embryonic development of the zebrafish. Dev. Dynam. 203, 253-310.
16. Liu, R.Z., Denovan-Wright, E.M., Degrave, A., Thisse, C., Thisse, B., Wright, J.M., 2004a. Spatio-temporal distribution of cellular retinol-binding protein gene transcripts (CRBPI and CRBPII) in the developing and adult zebrafish (Danio rerio). Eur. J. Biochem. 271 (2), 339-348.
17. Liu, R.-Z., Denovan-Wright, E.M., Degrave, A., Thisse, C., Thisse, B., Wright, J.M., 2004b. Differential expression of duplicate genes for brain-type fatty acidbinding proteins (fabp7a and fabp7b) during early development of the CNS in zebrafish (Danio rerio). Gene Expr. Patterns 4, 379-387.
18. Liu, R.-Z., Sun, Q., Thisse, C., Thisse, B., Denovan-Wright, E.M., Degrave, A., Wright, J.M., 2005a. The cellular retinol-binding protein genes are duplicated and differentially transcribed in the developing and adult zebrafish (Danio rerio). Mol. Biol. Evol. 22, 469-477.
19. Liu, R.-Z., Sharma, M.K., Sun, Q., Thisse, C., Thisse, B., Denovan-Wright, E.M., Wright, J.M., 2005b. Retention of the duplicated cellular retinoic acid-binding protein 1 genes (crabp1a and crabp1b) in the zebrafish genome by subfunctionalization of tissue specific expression. FEBS J. 272, 3561-3571.
20. Mulley, J., Holland, P., 2004. Small genome, big insights. Nature 431, 916-917.
21. Noy, N., 2000. Retinoid binding proteins: Mediators of retinoid action. Biochem. J. 348, 481-495.
22. Postlethwait, J.H., Woods, I.G., Ngo-Hazelett, P., Yan, Y.-L., Kelly, P.D., Chu, F., Huang, H., Hill-Force, A., Talbot, W.S., 2000. Zebrafish comparative genomics and the origin of vertebrate chromosomes. Genome Res. 10, 1890-1902.
23. Sharma, M.K., Saxena, V., Liu, R.-Z., Thisse, C., Thisse, B., Denovan-Wright, E.M., Wright, J.M., 2005. Differential expression of the duplicated cellular retinoic acid-binding protein 2 genes (crabp2a and crabp2b) during zebrafish embryonic development. Gene Expr. Patterns 5, 371-379. (Pubitemid 40124552)
24. Sharma, M.K., Liu, R.-Z., Thisse, C., Thisse, B., Denovan-Wright, E.M., Wright, J.M., 2006. Hierarchical subfunctionalization of fabp1a, fabp1b and fabp10 tissuespecific expression may account for retention of these duplicated genes in the zebrafish (Danio rerio) genome. FEBS J. 273, 3216-3229.
25. Tamura, K., Dudley, J., Nei, M., Kumar, S., 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599.
26. Tang, R., Dodd, A., Lai, D., McNabb, W.C., Love, D.R., 2007. Validation of zebrafish (Danio rerio) reference genes for quantitative real-time RT-PCR normalization. Acta Bioch. Bioph. Sin. 39, 384-390.
27. Taylor, J.S., Braasch, I., Frickey, T., Meyer, A., Van de Peer, Y., 2003. Genome duplication, a trait shared by 22000 species of ray-finned fish. Genome Res. 13, 382-390.
28. Taylor, J.S., Van de Peer, Y., Braasch, I., Meyer, A., 2001. Comparative genomics provides evidence for an ancient genome duplication event in fish. Philos. Trans. R. Soc. Lond. B. Biol. 356, 1661-1679.
29. Thisse, B., Thisse, C., 2004. Fast Release Clones: A High Throughput Expression Analysis. ZFIN Direct Data Submission (http://zfin.org).
30. Thisse, C., Thisse, B., 2008. High-resolution in situ hybridization to whole-mount zebrafish embryos. Nat. Protoc. 3, 59-69.
31. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
32. Van de Peer, Y., 2004. Tetraodon genome confirms takifugu findings: Most fish are ancient polyploids. Genome Biol. 5, 250.
33. Venkatachalam, A.B., Thisse, C., Thisse, B., Wright, J.M., 2009. Differential tissuespecific distribution of transcripts for the duplicated fatty acid-binding protein 10 (fabp10) genes in embryos, larvae and adult zebrafish (Danio rerio). FEBS J. 276, 6787-6797.
34. Vogel, A., Mendelsohn, C.L., Mettz, J.R., Piantedosi, S., Waldburger, C., Gottesmand, M.E., Blaner, W.S., 2001. Characterization of a new member of the fatty acidbinding protein family that binds all-trans-retinol. J. Biol. Chem. 276, 1353-1360.
35. Westerfield, M., 1995. The Zebrafish Book: A Guide for the Laboratory Use of Zebrafish (Danio rerio), 3rd ed. University of Oregon Press, Eugene, OR.
36. Woods, I.G., Kelly, P.D., Chu, F., Ngo-Hazelett, P., Yan, Y.-L., Huang, H., Postlethwait, J.H., Talbot, W.S., 2000. A comparative map of the zebrafish genome. Genome Res. 10, 1903-1914.
37. Zizola, C.F., Schwartz, G.J., Vogel, S., 2008. Cellular retinol-binding protein type III is a PPARγ target gene and plays a role in lipd metabolism. Am. J. Physiol. Endocrinol. Metab. 295, 1358-1368.