Molecular evolution of zebrafish dnmt3 genes and thermal plasticity of their expression during embryonic development

Gene

Volumn 500, Issue 1, 2012, Pages 93-100

  Campos, Catarina ^a,b   Valente, Luisa M P ^b   Fernandes, Jorge M O ^a  

^a NORD UNIVERSITY   (Norway)

^b UNIVERSITY OF PORTO   (Portugal)

Author keywords

Danio rerio; Embryonic development; Epigenetic regulation; Methyltransferases; Positive selection

Indexed keywords

DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; MESSENGER RNA;

ANIMAL TISSUE; ARTICLE; BLASTULA; EMBRYO; EMBRYO DEVELOPMENT; EPIGENETICS; FEMALE; GENE EXPRESSION REGULATION; GONAD; MALE; MOLECULAR EVOLUTION; MOUTH; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; TELEOST; TEMPERATURE SENSITIVITY; THERMAL PLASTICITY; ZEBRA FISH;

ANIMALS; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; EVOLUTION, MOLECULAR; FEMALE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HUMANS; MALE; PHYLOGENY; TERMINOLOGY AS TOPIC; ZEBRAFISH;

DANIO RERIO; MAMMALIA; TELEOSTEI; VERTEBRATA;

EID: 84860328637     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.03.041     Document Type: Article

References (41)

1. Burstein E., et al. COMMD proteins, a novel family of structural and functional homologs of MURR1. J. Biol. Chem. 2005, 280:22222-22232.
2. Campos C., Valente L.M., Borges P., Bizuayehu T., Fernandes J.M. Dietary lipid levels have a remarkable impact on the expression of growth-related genes in Senegalese sole (Solea senegalensis Kaup). J. Exp. Biol. 2010, 213:200-209.
3. Chen T., Ueda Y., Xie S., Li E. A novel Dnmt3a isoform produced from an alternative promoter localizes to euchromatin and its expression correlates with active de novo methylation. J. Biol. Chem. 2002, 277:38746-38754.
4. Chen T., Ueda Y., Dodge J.E., Wang Z., Li E. Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol. Cell. Biol. 2003, 23:5594-5605.
5. Fernandes J.M., et al. Myogenin in model pufferfish species: comparative genomic analysis and thermal plasticity of expression during early development. Comp. Biochem. Physiol. Part D Genomics Proteomics 2006, 1:35-45.
6. Fernandes J.M., MacKenzie M.G., Kinghorn J.R., Johnston I.A. FoxK1 splice variants show developmental stage-specific plasticity of expression with temperature in the tiger pufferfish. J. Exp. Biol. 2007, 210:3461-3472.
7. Fernandes J.M., Mommens M., Hagen O., Babiak I., Solberg C. Selection of suitable reference genes for real-time PCR studies of Atlantic halibut development. Comp. Biochem. Physiol. B 2008, 150:23-32.
8. Fernandes J.M., Ruangsri J., Kiron V. Atlantic cod piscidin and its diversification through positive selection. PLoS One 2010, 5:e9501.
9. Goll M.G., Bestor T.H. Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem. 2005, 74:481-514.
10. Gowher H., Liebert K., Hermann A., Xu G.L., Jeltsch A. Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J. Biol. Chem. 2005, 280:13341-13348.
11. Jaillon O., et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 2004, 431:946-957.
12. Johnston I.A., et al. Embryonic temperature affects muscle fibre recruitment in adult zebrafish: genome-wide changes in gene and microRNA expression associated with the transition from hyperplastic to hypertrophic growth phenotypes. J. Exp. Biol. 2009, 212:1781-1793.
13. Kaneda M., et al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 2004, 429:900-903.
14. Kasahara M. The 2R hypothesis: an update. Curr. Opin. Immunol. 2007, 19:547-552.
15. Katoh M. Identification and characterization of ASXL2 gene in silico. Int. J. Oncol. 2003, 23:845-850.
16. Kimmel C.B., Ballard W.W., Kimmel S.R., Ullmann B., Schilling T.F. Stages of embryonic development of the zebrafish. Dev. Dyn. 1995, 203:253-310.
17. Li J.Y., et al. Synergistic function of DNA methyltransferases Dnmt3a and Dnmt3b in the methylation of Oct4 and Nanog. Mol. Cell. Biol. 2007, 27:8748-8759.
18. Linhart H.G., et al. Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing. Genes Dev. 2007, 21:3110-3122.
19. Lynch M., Force A. The probability of duplicate gene preservation by subfunctionalization. Genetics 2000, 154:459-473.
20. MacKay A.B., Mhanni A.A., McGowan R.A., Krone P.H. Immunological detection of changes in genomic DNA methylation during early zebrafish development. Genome 2007, 50:778-785.
21. Martin C.C., Laforest L., Akimenko M.A., Ekker M. A role for DNA methylation in gastrulation and somite patterning. Dev. Biol. 1999, 206:189-205.
22. McCurley A.T., Callard G.V. Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment. BMC Mol. Biol. 2008, 9:102.
23. Mhanni A.A., McGowan R.A. Global changes in genomic methylation levels during early development of the zebrafish embryo. Dev. Genes Evol. 2004, 214:412-417.
24. Nagasawa K., Lazado C., Fernandes J.M.O. Validation of endogenous reference genes for qPCR quantification of muscle transcripts in Atlantic cod subjected to different photoperiod regimes. Aquaculture 2012, vol. 1:81-92. InTech, Croatia. Z.A. Muchlisin (Ed.).
25. Nguyen S., Meletis K., Fu D., Jhaveri S., Jaenisch R. Ablation of de novo DNA methyltransferase Dnmt3a in the nervous system leads to neuromuscular defects and shortened lifespan. Dev. Dyn. 2007, 236:1663-1676.
26. Okano M., Bell D.W., Haber D.A., Li E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999, 99:247-257.
27. Pennetier S., et al. MATER protein expression and intracellular localization throughout folliculogenesis and preimplantation embryo development in the bovine. BMC Dev. Biol. 2006, 6:26.
28. Pond S.L., Frost S.D. A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol. Biol. Evol. 2005, 22:478-485.
29. Qiu C., Sawada K., Zhang X., Cheng X. The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat. Struct. Biol. 2002, 9:217-224.
30. Rai K., et al. Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development. Mol. Cell. Biol. 2006, 26:7077-7085.
31. Rai K., et al. Dnmt2 functions in the cytoplasm to promote liver, brain, and retina development in zebrafish. Genes Dev. 2007, 21:261-266.
32. Rai K., et al. Dnmt3 and G9a cooperate for tissue-specific development in zebrafish. J. Biol. Chem. 2010, 285:4110-4121.
33. Ravi V., Venkatesh B. Rapidly evolving fish genomes and teleost diversity. Curr. Opin. Genet. Dev. 2008, 18:544-550.
34. Reik W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 2007, 447:425-432.
35. Shimoda N., Yamakoshi K., Miyake A., Takeda H. Identification of a gene required for de novo DNA methylation of the zebrafish no tail gene. Dev. Dyn. 2005, 233:1509-1516.
36. Smith T.H., Collins T.M., McGowan R.A. Expression of the dnmt3 genes in zebrafish development: similarity to Dnmt3a and Dnmt3b. Dev. Genes Evol. 2011, 220:347-353.
37. Ueda Y., Okano M., Williams C., Chen T., Georgopoulos K., Li E. Roles for Dnmt3b in mammalian development: a mouse model for the ICF syndrome. Development 2006, 133:1183-1192.
38. Whitlock K.E., Smith K.M., Kim H., Harden M.V. A role for foxd3 and sox10 in the differentiation of gonadotropin-releasing hormone (GnRH) cells in the zebrafish Danio rerio. Development 2005, 132:5491-5502.
39. Xie S., et al. Cloning, expression and chromosome locations of the human DNMT3 gene family. Gene 1999, 236:87-95.
40. Yang S.-Y., He X.-Y., Schulz H. 3-Hydroxyacyl-CoA dehydrogenase and short chain 3-hydroxyacyl-CoA dehydrogenase in human health and disease. FEBS J. 2005, 272:4874-4883.
41. Yokomine T., Hata K., Tsudzuki M., Sasaki H. Evolution of the vertebrate DNMT3 gene family: a possible link between existence of DNMT3L and genomic imprinting. Cytogenet. Genome Res. 2006, 113:75-80.