DNA methylation levels analysis in four tissues of sea cucumber Apostichopus japonicus based on fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) during aestivation

Comparative Biochemistry and Physiology Part - B: Biochemistry and Molecular Biology

Volumn 181, Issue 1, 2015, Pages 26-32

  Zhao, Ye ^a,b   Chen, Muyan ^c   Storey, Kenneth B ^d   Sun, Lina ^a   Yang, Hongsheng ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c OCEAN UNIVERSITY OF CHINA   (China)

^d CARLETON UNIVERSITY   (Canada)

Author keywords

A. japonicus; Aestivation; DNA methylation; F MSAP

Indexed keywords

GENOMIC DNA; FLUORESCENT DYE;

ADULT; AESTIVATION; ANIMAL TISSUE; APOSTICHOPUS JAPONICUS; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; DNA MODIFICATION; DNA SEQUENCE; FLUORESCENCE; FLUORESCENCE LABELED METHYLATION SENSITIVE AMPLIFIED POLYMORPHISM; GENE SILENCING; INTESTINE; ISOSCHIZOMER; MUSCLE; NONHUMAN; PRIORITY JOURNAL; RESPIRATORY SYSTEM; ANIMAL; GENETIC POLYMORPHISM; GENETICS; METABOLISM; PHYSIOLOGY; STICHOPUS;

APOSTICHOPUS JAPONICUS; HOLOTHUROIDEA;

ANIMALS; DNA METHYLATION; ESTIVATION; FLUORESCENT DYES; GENE SILENCING; POLYMORPHISM, GENETIC; STICHOPUS;

EID: 84914177134     PISSN: 10964959     EISSN: 18791107     Source Type: Journal    
DOI: 10.1016/j.cbpb.2014.11.001     Document Type: Article

References (52)

1. Allen R.C., Zoghbi H., Moseley A., Rosenblatt H., Belmont J. Methylation of HpaII and Hha I sites near the polymorphic CAG repeat in the human androgen-receptor gene correlates with X chromosome inactivation. Am. J. Hum. Genet. 1992, 51:1229.
2. Angers B., Castonguay E., Massicotte R. Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after. Mol. Ecol. 2010, 19:1283-1295.
3. Bird A.P., Taggart M.H., Smith B.A. Methylated and unmethylated DNA compartments in the sea urchin genome. Cell 1979, 17(4):889-901.
4. Bird A.P., Taggart M.H. Variable patterns of total DNA and rDNA methylation in animals. Nucleic Acids Res. 1980, 8(7):1485-1497.
5. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002, 16:6-21.
6. Cao Z., Yang J. Analysis of the methylation in genome DNA from different tissues of Anodonta woodiana. Ecology and Environmental Sciences 2009, 18(6):2011-2016. (in Chinese).
7. Chen M., Zhang X., Liu J., Storey K.B. High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation. PLoS One 2013, 8:e76120.
8. Choe J. DNA Methylation in development. J. Genet. Med. 2008, 5:100-104.
9. Day J.J., Sweatt J.D. DNA methylation and memory formation. Nat. Neurosci. 2010, 13:1319-1323.
10. Gama-Sosa M.A., Wang R.Y., Kuo K.C., Gehrke C.W., Ehrlich M. The 5-methylcytosine content of highly repeated sequences in human DNA. Nucleic Acids Res. 1983, 11(10):3087-3095.
11. Gowher H., Leismann O., Jeltsch A. DNA of Drosophila melanogaster contains 5-methylcytosine. EMBO J. 2000, 19(24):6918-6923.
12. Grippo P., Iaccarino M., Parisi E., Scarano E. Methylation of DNA in developing sea urchin embryos. J. Mol. Biol. 1968, 36(2):195-208.
13. Guo T., Sun G., Yang J., Zhao Q., Li C. MSAP analysis of genome DNA methylation in different tissues of Apostichopus japonicus. Oceanol. Limnol. Sin. 2013, 44(1):77-82. (in Chinese).
14. Herrera C.M., Bazaga P. Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis. New Phytol. 2010, 187:867-876.
15. Huang J., Sun M. A modified AFLP with fluorescence-labelled primers and automated DNA sequencer detection for efficient fingerprinting analysis in plants. Biotechnol. Tech. 1999, 13:277-278.
16. Hudson N.J., Lonhienne T.G., Franklin C.E., Harper G.S., Lehnert S.A. Epigenetic silencers are enriched in dormant desert frog muscle. J. Comp. Physiol. B. 2008, 178:729-734.
17. Krivoruchko A., Storey K.B. Epigenetics in anoxia tolerance: a role for histone deacetylases. Mol. Cell. Biochem. 2010, 342:151-161.
18. Li X., Wang X. The histological observation of alimentary tract and respiratory tree in sea cucumber, Apostichopus japonicus during aestivation induced in lab. J. Dalian Fish. Univ. 2007, 22:81-85. (in Chinese).
19. Li R., Ding J., Zhang Y., Cheng Y., Cao X., Chang Y. Histological study on the digestive tract of the Apostichopus japonicus in aestivation. Mar. Environ. Sci. 2006, 4:004. (in Chinese).
20. Lo N., Li B., Ujvari B. DNA methylation in the termite Coptotermes lacteus. Insect. Soc. 2012, 59:257-261.
21. Loomis S.H. Diapause and estivation in sponges. Aestivation 2010, 231-243. Springer.
22. Morin P., Storey K.B. Mammalian hibernation: differential gene expression and novel application of epigenetic controls. Int. J. Dev. Biol. 2009, 53:433-442.
23. Pałyga J. Genetic and epigenetic regulation in hypometabolism. Hypometabolism: strategies of survival in vertebrates and invertebrates 2011, Research Signpost, Kerala, 183-202.
24. Patel C.V., Gopinathan K.P. Determination of trace amounts of 5-methylcytosine in DNA by reverse phase high-performance liquid chromatography. Anal. Biochem. 1987, 164(1):164-169.
25. Regev A., Lamb M.J., Jablonka E. The role of DNA methylation in invertebrates: developmental regulation or genome defense?. Mol. Biol. Evol. 1998, 15(7):880-891.
26. Reyna-Lopez G., Simpson J., Ruiz-Herrera J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol. Gen. Genet. 1997, 253:703-710.
27. Seibel B.A., Häfker N.S., Trübenbach K., Zhang J., Tessier S.N., Pörtner H.O., Rosa R., Storey K.B. Metabolic suppression during protracted exposure to hypoxia in the jumbo squid, Dosidicus gigas, living in an oxygen minimum zone. J. Exp. Biol. 2014, 217(14):2555-2568.
28. Sha A., Lin X., Huang J., Zhang D. Analysis of DNA methylation related to rice adult plant resistance to bacterial blight based on methylation-sensitive AFLP (MSAP) analysis. Mol. Gen. Genet. 2005, 273:484-490.
29. Shan X., Wang X., Yang G., Wu Y., Su S., Li S., Liu H., Yuan Y. Analysis of the DNA methylation of maize (Zea mays L.) in response to cold stress based on methylation-sensitive amplified polymorphisms. J. Plant Biol. 2013, 56:32-38.
30. Simpson V.J., Johnson T.E., Hammen R.F. Caenorhabditis elegans DNA does not contain 5-methylcytosine at any time during development or aging. Nucleic Acids Res. 1986, 14(16):6711-6719.
31. Steven B.R., Mackenzie R.G. Is there a relationship between DNA methylation and phenotypic plasticity in invertebrates?. Front. Physiol. 2012, 2(116):1-5.
32. Storey K.B., Storey J.M. Metabolic rate depression in animals: transcriptional and translational controls. Biol. Rev. 2004, 79:207-233.
33. Storey K.B., Storey J.M. Tribute to PL Lutz: Putting life on 'pause'-molecular regulation of hypometabolism. J. Exp. Biol. 2007, 210:1700-1714.
34. Storey K.B., Storey J.M. Metabolic regulation and gene expression during aestivation. Aestivation: Molecular and Physiological Aspects 2010, 25-45. Springer, Heidelberg. C.A. Navas, J.E. Carvalho (Eds.).
35. Sun Y., Hou R., Fu X., Sun C., Wang S., Wang C., Li N., Zhang L., Bao Z. Genome-wide analysis of DNA methylation in five tissues of zhikong scallop, Chlamys farreri. PLoS One 2014, 9(1):e86232.
36. Takemae N., Nakaya F., Motokawa T. Low oxygen consumption and high body content of catch connective tissue contribute to low metabolic rate of sea cucumbers. Biol. Bull. 2009, 216(1):45-54.
37. Thurmond F., Trotter J. Morphology and biomechanics of the microfibrillar network of sea cucumber dermis. J. Exp. Biol. 1996, 199(8):1817-1828.
38. Tosi L., Aniello F., Geraci G., Branno M. DNA methyltransferase activity in the early stages of a sea urchin embryo - evidence of differential control. FEBS Lett. 1995, 361(1):115-117.
39. Tserel L., Limbach M., Saare M., Kisand K., Metspalu A., Milani L., Peterson P. CpG sites associated with NRP1, NRXN2 and miR-29b-2 are hypomethylated in monocytes during ageing. Immun. Ageing 2014, 11:1.
40. Turner B.M. Epigenetic responses to environmental change and their evolutionary implications. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2009, 364:3403-3418.
41. Tycko B. DNA methylation in genomic imprinting. Mutat. Res. Rev. Mutat. Res. 1997, 386:131-140.
42. Vos P., Hogers R., Bleeker M., Reijans M., Van de Lee T., Hornes M., Frijters A., Pot J., Peleman J., Kuiper M., Zabeau M. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995, 23(21):4407-4414.
43. Wang T., Yang H., Zhao H., Chen M., Wang B. Transcriptional changes in epigenetic modifiers associated with gene silencing in the intestine of the sea cucumber, Apostichopus japonicus (Selenka), during aestivation. Chin. J. Oceanol. Limnol. 2011, 29:1267-1274.
44. Xiong L., Xu C., Maroof M., Zhang Q. Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol. Gen. Genet. 1999, 261(3):439-446.
45. Xu Q., Zhang Y., Sun D., Wang Y., Yu Y. Analysis on DNA methylation of various tissues in chicken. Anim. Biotechnol. 2007, 18:231-241.
46. Yaish M.W., Peng M., Rothstein S.J. Global DNA methylation analysis using methyl-sensitive amplification polymorphism (MSAP). Arabidopsis Protocols 2014, 285-298. Springer.
47. Yang H., Yuan X., Zhou Y., Mao Y., Zhang T., Liu Y. Effects of body size and water temperature on food consumption and growth in the sea cucumber Apostichopus japonicus (Selenka) with special reference to aestivation. Aquac. Res. 2005, 36:1085-1092.
48. Yang H., Zhou Y., Zhang T., Yuan X., Li X., Liu Y., Zhang F. Metabolic characteristics of sea cucumber Apostichopus japonicus (Selenka) during aestivation. J. Exp. Mar. Biol. Ecol. 2006, 330:505-510.
49. Yang C., Zhang M., Niu W., Yang R., Zhang Y., Qiu Z., Sun B., Zhao Z. Analysis of DNA methylation in various swine tissues. PLoS One 2011, 6:e16229.
50. Yu T., Yang A., Wu B., Zhou L. Analysis of Chlamys farreri, Patinopecten yessoensis and their offspring using methylation- sensitive amplification polymorphism (MSAP). Journal of Fisheries of China 2010, 34(9):1335-1342. (in Chinese).
51. Yuan X., Yang H., Wang L., Zhou Y., Zhang T., Liu Y. Effects of aestivation on the energy budget of sea cucumber Apostichopus japonicus (Selenka)(Echinodermata: Holothuroidea). Acta Ecol. Sin. 2007, 27:3155-3161.
52. Zhao Y., Chen M., Su L., Wang T., Liu S., Yang H. Molecular cloning and expression-profile analysis of sea cucumber DNA (cytosine-5)-methyltransferase 1 and methyl-CpG binding domain type 2/3 genes during aestivation. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 2013, 165:26-35.