Do not put all teleosts in one net: Focus on the sox2 and pou2 genes

Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology

Volumn 164, Issue 2, 2013, Pages 69-79

  Marandel, Lucie ^a   Labbe, Catherine ^a   Bobe, Julien ^a   Jammes, Hélène ^b   Lareyre, Jean Jaques ^a   Le Bail, Pierre Yves ^a  

^a Campus de Beaulieu   (France)

^b INRA Institut National de la Recherche Agronomique   (France)

Author keywords

Development; DNA methylation; Gamete; Goldfish; Pou5f1

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR POU2; TRANSCRIPTION FACTOR SOX2; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARTICLE; CELL DIFFERENTIATION; CELL MATURATION; COMPUTER MODEL; CONSERVATION GENETICS; CONTROLLED STUDY; CPG ISLAND; CYPRINIFORMES; DEVELOPMENTAL STAGE; DNA DETERMINATION; DNA FLANKING REGION; DNA METHYLATION; EMBRYO DEVELOPMENT; FEMALE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC VARIABILITY; GOLDFISH; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN MOTIF; TELEOST; TETRAODONTIFORMES; ZEBRA FISH;

EID: 84870679277     PISSN: 10964959     EISSN: 18791107     Source Type: Journal    
DOI: 10.1016/j.cbpb.2012.10.005     Document Type: Article

References (54)

1. Aegerter S., Jalabert B., Bobe J. Large scale real-time PCR analysis of mRNA abundance in rainbow trout eggs in relationship with egg quality and post-ovulatory ageing. Mol. Reprod. Dev. 2005, 72:377-385.
2. Athanasiadou R., de Sousa D., Myant K., Merusi C., Stancheva I., Bird A. Targeting of de novo DNA methylation throughout the Oct-4 gene regulatory region in differentiating embryonic stem cells. PLoS One 2010, 5:e9937.
3. Bailey T.L., Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 1994, 2:28-36.
4. Bowles J., Schepers G., Koopman P. Phylogeny of the SOX family of developmental transcription factors based on sequence and structural indicators. Dev. Biol. 2000, 227:239-255.
5. Burgess S., Reim G., Chen W., Hopkins N., Brand M. The zebrafish spiel-ohne-grenzen (spg) gene encodes the POU domain protein Pou2 related to mammalian Oct4 and is essential for formation of the midbrain and hindbrain, and for pre-gastrula morphogenesis. Development 2002, 129:905-916.
6. Cui J., Shen X., Zhao H., Nagahama Y. Genome-wide analysis of Sox genes in Medaka (Oryzias latipes) and their expression pattern in embryonic development. Cytogenet. Genome Res. 2011, 134:283-294.
7. Desvignes T., Pontarotti P., Fauvel C., Bobe J. Nme protein family evolutionary history, a vertebrate perspective. BMC Evol. Biol. 2009, 9:256.
8. Desvignes T., Fauvel C., Bobe J. The nme gene family in zebrafish oogenesis and early development. Naunyn. Schmiedebergs Arch. Pharmacol. 2011, 384:439-449.
9. Feldman N., Gerson A., Fang J., Li E., Zhang Y., Shinkai Y., Cedar H., Bergman Y. G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat. Cell Biol. 2006, 8:188-194.
10. Flores M.V., Hall C.J., Davidson A.J., Singh P.P., Mahagaonkar A.A., Zon L.I., Crosier K.E., Crosier P.S. Intestinal differentiation in zebrafish requires Cdx1b, a functional equivalent of mammalian Cdx2. Gastroenterology 2008, 135:1665-1675.
11. Frankenberg S., Pask A., Renfree M.B. The evolution of class V POU domain transcription factors in vertebrates and their characterisation in a marsupial. Dev. Biol. 2010, 337:162-170.
12. Gabillard J.C., Rescan P.-Y., Fauconneau B., Weil C., Le Bail P.-Y. Effect of temperature on gene expression of the GH/IGF system during embryonic development in rainbow trout (Oncorhynchus mykiss). J. Exp. Zool. A Comp. Exp. Biol. 2003, 298:134-142.
13. Gautier A., Le Gac F., Lareyre J.J. The gsdf gene locus harbors evolutionary conserved and clustered genes preferentially expressed in fish previtellogenic oocytes. Gene 2011, 472:7-17.
14. Geiman T.M., Robertson K.D. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together?. J. Cell. Biochem. 2002, 87:117-125.
15. Gouret P., Vitiello V., Balandraud N., Gilles A., Pontarotti P., Danchin E.G. FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform. BMC Bioinforma. 2005, 6:198.
16. Guth S.I.E., Wegner M. Having it both ways: Sox protein function between conservation and innovation. Cell. Mol. Life Sci. 2008, 65:3000-3018.
17. Hauptmann G., Gerster T. Pou2 - a zebrafish gene active during cleavage stages and in the early hindbrain. Mech. Dev. 1995, 51:127-138.
18. Heinemeyer T., Wingender E., Reuter I., Hermjakob H., Kel A.E., Kel O.V., Ignatieva E.V., Ananko E.A., Podkolodnaya O.A., Kolpakov F.A., Podkolodny N.L., Kolchanov N.A. Databases on transcriptional regulation: TRANSFAC TRRD and COMPEL. Nucleic Acids Res. 1998, 26:362-367.
19. Iwafuchi-Doi M., Yoshida Y., Onichtchouk D., Leichsenring M., Driever W., Takemoto T., Uchikawa M., Kamachi Y., Kondoh H. The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates. Dev. Biol. 2011, 352:354-366.
20. Kamachi Y., Iwafuchi M., Okuda Y., Takemoto T., Uchikawa M., Kondoh H. Evolution of non-coding regulatory sequences involved in the developmental process: reflection of differential employment of paralogous genes as highlighted by Sox2 and group B1 Sox genes. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 2009, 85:55-68.
21. Kane D.A., Kimmel C.B. The zebrafish midblastula transition. Development 1993, 119:447-456.
22. Kass S.U., Pruss D., Wolffe A.P. How does DNA methylation repress transcription?. Trends Genet. 1997, 13:444-449.
23. Lachnit M., Kur E., Driever W. Alterations of the cytoskeleton in all three embryonic lineages contribute to the epiboly defect of Pou5f1/Oct4 deficient MZspg zebrafish embryos. Dev. Biol. 2008, 315:1-17.
24. Le Bail P.-Y., Depince A., Chenais N., Mahe S., Maisse G., Labbe C. Optimization of somatic cell injection in the perspective of nuclear transfer in goldfish. BMC Dev. Biol. 2010, 10:64.
25. Lindeman L.C., Winata C.L., Aanes H., Mathavan S., Alestrom P., Collas P. Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos. Int. J. Dev. Biol. 2010, 54:803-813.
26. Lunde K., Belting H.G., Driever W. Zebrafish pou5f1/pou2, homolog of mammalian Oct4, functions in the endoderm specification cascade. Curr. Biol. 2004, 14:48-55.
27. Ma S.S., Huang W.X., Zhang L., Zhao S.F., Tong Y., Liu Z.H., Sun L., Chen H.Y., Luo C. Germ cell-specific DNA methylation and genome diploidization in primitive vertebrates. Epigenetics 2011, 6:1471-1480.
28. Macleod D., Clark V.H., Bird A. Absence of genome-wide changes in DNA methylation during development of the zebrafish. Nat. Genet. 1999, 23:139-140.
29. Marandel L., Labbé C., Bobe J., Le Bail P.-Y. Evolutionary history of c-myc in teleosts and duplicated c-myca genes characterization in goldfish embryos. Mol. Reprod. Dev. 2012, 79:85-96.
30. Marandel L., Labbé C., Bobe J., Le Bail P.-Y. nanog 5'-upstream sequence, DNA methylation, and expression in gametes and early embryo reveal striking differences between teleosts and mammals. Gene 2012, 49:130-137.
31. 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.
32. Morrison G.M., Brickman J.M. Conserved roles for Oct4 homologues in maintaining multipotency during early vertebrate development. Development 2006, 133:2011-2022.
33. Nguyen D.H., D'haeseleer P. Deciphering principles of transcription regulation in eukaryotic genomes. Mol. Syst. Biol. 2006, 2:0012.
34. Niwa H., Sekita Y., Tsend-Ayush E., Grutzner F. Platypus Pou5f1 reveals the first steps in the evolution of trophectoderm differentiation and pluripotency in mammals. Evol. Dev. 2008, 10:671-682.
35. Okazawa H., Okamoto K., Lshino F., Ishino-Kaneko T., Takeda S., Toyoda Y., Muramatsu M., Hamada H. The oct3 gene, a gene for an embryonic transcription factor, is controlled by a retinoic acid repressible enhancer. EMBO J. 1991, 10:2997-3005.
36. Okuda Y., Yoda H., Uchikawa M., Furutani-Seiki M., Takeda H., Kondoh H., Kamachi Y. Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution. Dev. Dyn. 2006, 235:811-825.
37. Okuda Y., Ogura E., Kondoh H., Kamachi Y. B1 SOX coordinate cell specification with patterning and morphogenesis in the early zebrafish embryo. PLoS Genet. 2010, 6:e1000936.
38. Onichtchouk D., Geier F., Polok B., Messerschmidt D.M., Mossner R., Wendik B., Song S., Taylor V., Timmers J., Driever W. Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development. Mol. Syst. Biol. 2010, 6:354.
39. Parvin M.S., Okuyama N., Inoue F., Islam M.E., Kawakami A., Takeda H., Yamasu K. Autoregulatory loop and retinoic acid repression regulate pou2/pou5f1 gene expression in the zebrafish embryonic brain. Dev. Dyn. 2008, 237:1373-1388.
40. Pikarsky E., Sharir H., Ben-Shushan E., Bergman Y. Retinoic acid represses Oct-3/4 gene expression through several retinoic acid-responsive elements located in the promoter-enhancer region. Mol. Cell. Biol. 1994, 14:1026-1038.
41. Pownall M.E., Gustafsson M.K., Emerson C.P. Myogenic regulatory factors and the specification of muscle progenitors in vertebrate embryos. Annu. Rev. Cell Dev. Biol. 2002, 18:747-783.
42. Reim G., Brand M. Maternal control of vertebrate dorsoventral axis formation and epiboly by the POU domain protein Spg/Pou2/Oct4. Development 2006, 133:2757-2770.
43. Reim G., Mizoguchi T., Stainier D.Y., Kikuchi Y., Brand M. The POU domain protein spg (pou2/Oct4) is essential for endoderm formation in cooperation with the HMG domain protein casanova. Dev. Cell 2004, 6:91-101.
44. Sanchez-Sanchez A.V., Camp E., Garcia-Espana A., Leal-Tassias A., Mullor J.L. Medaka Oct4 is expressed during early embryo development, and in primordial germ cells and adult gonads. Dev. Dyn. 2010, 239:672-679.
45. Schier A., Talbot W. Molecular genetics of axis formation in zebrafish. Annu. Rev. Genet. 2005, 39:561-613.
46. Schoorlemmer J., Jonk L., Shen S., van Puijenbroek A., Feijen A., Kruijer W. Regulation of Oct-4 gene expression during differentiation of EC cells. Mol. Biol. Rep. 1995, 21:129-140.
47. Sekido R., Murai K., Funahashi J., Kamachi Y., Fujisawa-Sehara A., Nabeshima Y., Kondoh H. The delta-crystallin enhancer-binding protein delta-EF1 is a repressor of E2-box-mediated gene activation. Mol. Cell. Biol. 1994, 14:5692-5700.
48. Takeda H., Matsuzaki T., Oki T., Miyagawa T., Amanuma H. A novel POU domain gene, zebrafish pou2: expression and roles of two alternatively spliced twin products in early development. Genes Dev. 1994, 8:45-59.
49. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
50. Timmers C., Sharma N., Opavsky R., Maiti B., Wu L., Wu J., Orringer D., Trikha P., Saavedra H.I., Leone G. E2f1, E2f2, and E2f3 Control E2F target expression and cellular proliferation via a p53-dependent negative feedback loop. Mol. Cell. Biol. 2007, 27:65-78.
51. Vaissiere T., Sawan C., Herceg Z. Epigenetic interplay between histone modifications and DNA methylation in gene silencing. Mutat. Res. 2008, 659:40-48.
52. Wiebe M.S., Wilder P.J., Kelly D., Rizzino A. Isolation, characterization, and differential expression of the murine Sox-2 promoter. Gene 2000, 246:383-393.
53. Wu S.F., Zhang H., Cairns B.R. Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome Res. 2011, 21:578-589.
54. Yamakoshi K., Shimoda N. De novo DNA methylation at the CpG island of the zebrafish no tail gene. Genesis 2003, 37:195-202.