Circadian expression of DNA methylation and demethylation genes in zebrafish gonads

References

• Adams CE, Woltering C, Alexander G. 2003. Epigenetic regulation of trophic morphology through feeding behavior in Arctic char, Salvelinus alpines. Biol J Linnean Soc. 78:43–49.
   Web of Science ®Google Scholar
• Aguilar-Arnal L, Sassone-Corsi P. 2013. The circadian epigenome: How metabolism talks to chromatin remodeling. Sci Direct. 25:170–76.
   Google Scholar
• Alila-Johansson A, Eriksson L, Soveri T, Laakso ML. 2004. Daily and annual variations of free fatty acid, glycerol and leptin plasma concentrations in goats (Capra hircus) under different photoperiods. Comp Biochem Phys A. 138:119–31.
   PubMed Web of Science ®Google Scholar
• Baker CF, Waner JI, Vieira EF, Taylor SR, Driver HS, Mitchell D. 2001. Sleep and 24 hour body temperatures: A comparison in young men, naturally cycling women and women taking hormonal contraceptives. J Physio. 530:565–74.
   PubMed Web of Science ®Google Scholar
• Balon EB. 1990. Epigenesis of an epigeneticist: the development of some alternative concepts on the early ontogeny and evolution of fishes. Guelph Ichthyol Rev. 1:1–48.
   Google Scholar
• Brown SE, Fraga MF, Weaver IC, Berdasco M, Szyf M. 2007. Variations in DNA methylation patterns during the cell cycle of HeLa cells. Epigenetics. 2:54–65.
   PubMed Web of Science ®Google Scholar
• Buhr ED, Yoo SH, Takahashi JS. 2010. Temperature as a universal resetting cue for mammalian circadian oscillators. Science. 330:379–85.
   PubMed Web of Science ®Google Scholar
• Campos C, Valente M, Fernandes J. 2012. Molecular evolution of zebrafish dnmt3 genes and thermal plasticity of their expression during embryonic development. Gene. 500:93–100.
   PubMed Web of Science ®Google Scholar
• Chunyu L, Chung M. 2015. Genetics and epigenetics of circadian rhythms and their potential roles in neuropsychiatric disorders. Neurosci Bull. 31:141–59.
   PubMed Web of Science ®Google Scholar
• Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. 2008. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 452:215–19.
   PubMed Web of Science ®Google Scholar
• Dhliwayo N, Sarras MP Jr, Luczkowski E, Mason SM, Intine RV. 2014. Parp inhibition prevents ten-eleven translocase enzyme activation and hyperglycemia-induced DNA demethylation. Diabetes. 63:3069–76.
   PubMed Web of Science ®Google Scholar
• Di Rosa V, López-Olmeda JF, Burguillo A, Frigato E, Bertolucci C, Piferrer F, Sánchez-Vázquez FJ. 2016. Daily rhythms of the expression of key genes involved in steroidogenesis and gonadal function in zebrafish. PloS One. 11(6):e0157716.
   PubMed Web of Science ®Google Scholar
• Feng D, Liu T, Sun Z, Bugge A, Mullican SE, Alenghat T, Liu XS, Lazar MA. 2011. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science. 331:1315–19.
   PubMed Web of Science ®Google Scholar
• Ferguson-Smith AC. 2011. Genomic imprinting: The emergence of an epigenetic paradigm. Nat Rev Genet. 12:565–75.
   PubMed Web of Science ®Google Scholar
• Froy O. 2010. Metabolism and circadian rhythms –Implications for obesity. Endocr Rev. 31:1–24.
   PubMed Web of Science ®Google Scholar
• Garaulet M, Gómez-Abellán P, Madrid JA. 2010. Chronobiology and obesity: The orchestra out of tune. Clin Lipidology. 5:181–88.
   Web of Science ®Google Scholar
• Hastings M, O`Neill J, Maywood ES. 2007. Circadian clocks: regulators of endocrine and metabolic rhythms. J Endocrinol. 195:187–98.
   PubMed Web of Science ®Google Scholar
• Ho D (2008). Morphological and physiological developmental consequences of epigenetic processes in the chicken embryo (Gallus gallus domesticus) and the zebrafish larva (Danio rerio). Challenges and Opportunities Dissertation (UMI microform 3352093, Copyright 2009 by ProQuest LLC). Univ. North Texas.
   Google Scholar
• Homma K, Hastings JW. 1989. Cell growth kinetics, division asymmetry and volume control at division in the marine dinoflagellate Gonyaulax polyhedra: a model of circadian clock control of the cell cycle. J Cell Sci. 92:303–18.
   PubMed Web of Science ®Google Scholar
• Honma K, Honma S, Wada T. 1987. Entrainment of human circadian rhythms by artificial bright light cycles. Experientia. 43:572–74.
   PubMedGoogle Scholar
• Huang W, Ramsey KM, Marcheva B, Bass J. 2011. Circadian rhythms, sleep, and metabolism. J Clin Invest. 121:2133–41.
   PubMed Web of Science ®Google Scholar
• Isorna E, De Pedro N, Valenciano A. 2017. Interplay between the endocrine and circadian systems in fishes. J Endocrinol. 232:141–59.
   PubMed Web of Science ®Google Scholar
• Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. 2010. Role of Tet proteins in 5 mC to 5 hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 466:1129–33.
   PubMed Web of Science ®Google Scholar
• Kamstra JH, Aleström P, Kooter JM. 2014. Zebrafish as a model to study the role of DNA methylation in environmental toxicology. Environ Sci Pollut R. 22:16262–76.
   PubMed Web of Science ®Google Scholar
• Levi F, Schibler U. 2007. Circadian rhythms: mechanisms and therapeutic implications. Anny Rev Pharmacol Toxicol. 47:593–628.
   PubMed Web of Science ®Google Scholar
• Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 462:315–22.
   PubMed Web of Science ®Google Scholar
• Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(T) (-Delta Delta C) method. Methods. 25:402–08.
   PubMed Web of Science ®Google Scholar
• López-Olmeda JF, Sánchez-Vázquez FJ. 2010. Biological clock in fish. In Taylor & Francis, eds. Feeding rhythms in fish: From behavioral to molecular approach. Enfield, NH, USA: 155–83.
   Google Scholar
• Mañanós E, Duncan N, Mylonas CC. 2008. Methods in reproductive aquaculture: marine and freshwater species. In Taylor & Francis, eds. Reproduction and control of ovulation, spermiation and spawning in cultured fish. FL, USA: 3–80.
   Google Scholar
• Martin CC, Larorest L, Akimenko MA. 1999. A role for DNA methylation in gastrulation and somite pattering. Dev Biol. 206:189–205.
   PubMed Web of Science ®Google Scholar
• Maury E, Ramsey KM, Bass J. 2010. Circadian rhythms and metabolic syndrome: From experimental genetics to human disease. Circ Res. 106:447–62.
   PubMed Web of Science ®Google Scholar
• Merrow M, Roenneberg T. 2004. Cellular clocks: coupled circadian and cell division cycles. Curr Biol. 14:25–26.
   PubMed Web of Science ®Google Scholar
• Mhanni AA, McGowan RA. 2004. Global changes in genomic methylation levels during early development of the zebrafish embryo. Dev Genes Evol. 214:412–17.
   PubMed Web of Science ®Google Scholar
• Mistlberger RE. 2009. Food-anticipatory circadian rhythms: Concepts and methods. Eur J of Neurosci. 30:1718–29.
   PubMed Web of Science ®Google Scholar
• Moore LD, Le T, Fan G. 2013. DNA methylation and its basic function. Neuropsychopharmacol. 38:23–38.
   PubMed Web of Science ®Google Scholar
• Nagorny C, Lyssenko V. 2012. Tired of diabetes genetics? Circadian rhythms and diabetes: the MTNR1B story?. Curr Diab Rep. 12:667–72.
   PubMed Web of Science ®Google Scholar
• Nagoshi E, Saini C, Bauer C, Laroche T, Naef F, Schibler U. 2004. Circadian gene expression in individual fibroblasts: Cell-autonomous and self sustained oscillators pass time to daughter cells. Cell. 119:693–705.
   PubMed Web of Science ®Google Scholar
• Navarro-Martín L, Blázquez M, Vinas J, Joly S, Piferrer F. 2009. Balancing the effects of rearing at low temperature during early development on sex ratios, growth and maturation in the European sea bass (Dicentrarchus labrax). Limitations and opportunities for the production of highly female-biased stocks. Aquacult. 296:347–58.
   Google Scholar
• Niehrs C, Schäfer A. 2012. Active DNA demethylation by Gadd45 and DNA repair Trends. Cell Biol. 22:220–27.
   Google Scholar
• Oliveira C, Soares F, Cabrita E, Pousao-Ferreira P, Sánchez-Vázquez FJ. 2009a. Lunar and daily spawning rhythms of Senegal sole (Solea senegalensis). J of Fish Biol. 75:61–74.
   PubMed Web of Science ®Google Scholar
• Oliveira C, Vera LM, López-Olmeda JF, Guzmán JM, Mañanós E, Ramos J, Sánchez-Vázquez FJ. 2009b. Monthly day/night changes and seasonal daily rhythms of sexual steroids in Senegal sole (Solea senegalensis) under natural fluctuating or controlled environmental conditions. Comp Biochem Physiol A. 152:168–75.
   PubMed Web of Science ®Google Scholar
• Ooi SK, Qui C, Bernstein E, Li K, Jia D, Yang Z, Erdjument-Bromage H, Tempst P, Lin SP, Allis CD, et al. 2007. DNMT3L connects unmethylated lysine 4 of histone H3 to de novomethylation of DNA. Nature. 448:714–17.
   PubMed Web of Science ®Google Scholar
• Panda S, Hogenesch JB, Kay SA. 2002. Circadian rhythms from flies to human. Nature. 417:329–35.
   PubMed Web of Science ®Google Scholar
• Paredes JF, López-Olmeda JF, Martínez FJ, Sánchez-Vázquez FJ. 2015. Daily rhythms of lipid metabolic gene expression in zebrafish liver: Response to light-dark and feeding cycles. Chronobiol Int. 10:1438–48.
   Google Scholar
• Peaston A, Whitelaw E. 2006. Epigenetics and phenotypic variation in mammals. Mamm Genome. 17:365–74.
   PubMed Web of Science ®Google Scholar
• Piferrer F. 2013. Epigenetics of sex determination and gonadogenesis. Dev Dyn. 242:360–70.
   PubMed Web of Science ®Google Scholar
• Piferrer F, Ribas L, Díaz N. 2012. Genomic approaches to study genetic and environmental influences on fish sex determination and differentiation. Mar Biotechnol. 14:591–604.
   PubMed Web of Science ®Google Scholar
• Pittman K, Yúfera M, Pavlidis M, Geffen AJ, Koven W, Ribeiro L, Zambonino-Infante JL, Tandler A. 2013. Fantastically plastic: Fish larvae equipped for a new world. Rev Aquacult. 5:224–67.
   Web of Science ®Google Scholar
• Portaluppi F, Smolensky M, Touitou Y. 2010. Ethics and methods for biological rhythm research in animal and human beings. Chronobiol Int. 27:1911–29.
   PubMed Web of Science ®Google Scholar
• Rensing L, Ruoff P. 2002. Temperature effect on entrainment, phase shifting, and amplitude of circadian clocks and its molecular bases. Chronobiol Int. 19:807–64.
   PubMed Web of Science ®Google Scholar
• Ripperger JA, Jud C, Albrecht U. 2011b. The daily rhythm of mice. Circadian Rhythms. 585:1384–92.
   Google Scholar
• Ripperger JA, Merrow M. 2011a. Perfect timing: Epigenetic regulation of the circadian clock. Febs Lett. 585:1406–11.
   PubMed Web of Science ®Google Scholar
• Rountree MR, Selker EU. 1997. DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa. Genes Dev. 11:2383–95.
   PubMed Web of Science ®Google Scholar
• Sánchez-Vázquez FJ, Madrid JA, Zamora S, Tabata M. 1997. Feeding entrainment of locomotor activity rhythms in the goldfish is mediated by a feeding-entrainable circadian oscillator. J Comp Physiol A. 181:121–32.
   Web of Science ®Google Scholar
• Savvidis C, Koutsilieris M. 2012. Circadian rhythm disruption in cancer biology. Mol Med. 18:1249–60.
   PubMed Web of Science ®Google Scholar
• Schwerte T, Voigt S, Pelster B. 2005. Epigenetic variations in early cardiovascular performance and hematopoiesis can be explained by maternal and clutch effects in developing zebrafish (Danio rerio). Comp Biochem Physiol Mol Integr Physiol. 141:200–09.
   PubMed Web of Science ®Google Scholar
• Sherman H, Genzer Y, Cohen R, Chapnik N, Madar Z, Froy O. 2012. Timed high-fat diet resets circadian metabolism and prevents obesity. Faseb J. 26:3493–502.
   PubMed Web of Science ®Google Scholar
• So WK, Kwok HF, Ge W. 2005. Zebrafish gonadotropins and their receptors: II. Cloning and characterization of zebrafish follicle-stimulating hormone and luteinizing hormone subunits- their spatial-temporal expression patterns and receptor specificity. Biol Reprod. 72:1382–96.
   PubMed Web of Science ®Google Scholar
• Swanson GR, Burgess HJ, Keshavarzian A. 2011. Sleep disturbances and inflammatory bowel disease: A potential trigger for disease flare? Expert Rev Clin Immunol. 7:29–36.
   PubMed Web of Science ®Google Scholar
• Villamizar N, Ribas L, Piferrer F, Vera LM, Sánchez-Vázquez FJ. 2012. Impact of daily thermocycles on hatching rhythms, larval performance and sex differentiation of zebrafish. PloS One. 7(12):e52153.
   PubMed Web of Science ®Google Scholar
• Whitmore D, Foulkes NS, Sassone-Corsi P. 2000. Lights acts directly on organs and cells in culture to set the vertebrate circadian clock. Nature. 404:87–91.
   PubMed Web of Science ®Google Scholar
• Whitmore D, Foulkes NS, Strähle U, Sassone-Corsi P. 1998. Zebrafish Clock rhythmic expression reveal independent peripheral circadian oscillators. Nat Neurosci. 1:701–107.
   PubMed Web of Science ®Google Scholar
• Williams KT, Schalinske KL. 2012. Tissue-specific alterations of methyl group metabolism with DNA hypermethylation in the Zucker (type 2) diabetic fatty rat. Diabetes Metab Res Rev. 28:123–31.
   PubMed Web of Science ®Google Scholar
• Xia L, Ma S, Zhang Y, Wang T, Zhou M, Wang Z, Zhang J. 2015. Daily variation in global and local DNA methylation in mouse livers. PloS One. 10:e0118101.
   PubMed Web of Science ®Google Scholar
• Yaron Z, Levavi-Sivan B. 2011. encyclopedia of fish physiology: From genome to environment. In:Endocrine regulation of fish reproduction. San Diego, USA: Academic press. p. 1500–08.
   Google Scholar
• Yoshizaki G, Okutsu T, Ichikawa M, Hayashi M, Takeuchi Y. 2010. Sexual plasticity of rainbow trout germ cells. Anim Repro. 3:187–96.
   Google Scholar
• Zhang L, Lu X, Lu J, Liang H, Dai Q, Xu GL, Luo C, Jiang H, He C. 2012. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat Chem Biol. 8:328–30.
   PubMed Web of Science ®Google Scholar