Occurrence of DNA methylation in Daphnia magna and influence of multigeneration Cd exposure.

Most of the research on the epigenetic phenomenon of DNA methylation has been performed with vertebrates and plants. Knowledge on DNA methylation in Daphnia magna, a key test organism in aquatic toxicology, is completely lacking. Through epigenetic inheritance, effects of transient chemical exposure could be transferred to non-exposed generations, which could have a major impact on ecological risk assessment procedures. In this study, we determined if CpG methylation occurs in D. magna and if this can be influenced by exposure to toxic substances. Homologs of human DNA methyltransferases DNMT1, DNMT2 and DNMT3A were found in the partially available D. magna genome. Using an optimized "Amplification of Intermethylated Sites (AIMS)" technique, two methylated fragments were discovered in D. magna DNA. No homology was found for these sequences. The methylation and the D. magna origin of the fragments were confirmed with Southern analysis. This optimized AIMS technique was then applied to DNA of D. magna which were exposed to 180 microg/L Cd for two generations. Exposure resulted in a significant decrease in reproduction. The same methylated fragments with the same band intensity were observed in DNA of both non-exposed and exposed daphnids. As such, it could not be demonstrated that Cd exposure altered DNA methylation. However, the presence of DNA methylation in D. magna shows that potentially epigenetic effects may occur in this species.

[1]  T. Tuschl,et al.  Mechanisms of gene silencing by double-stranded RNA , 2004, Nature.

[2]  F. Pelliccia,et al.  DNA methylation, histone H3 methylation, and histone H4 acetylation in the genome of a crustacean. , 2006, Genome.

[3]  I. Henderson,et al.  Gardening the genome: DNA methylation in Arabidopsis thaliana , 2005, Nature Reviews Genetics.

[4]  W Dean,et al.  DNA methylation and mammalian epigenetics , 2001, Electrophoresis.

[5]  S. Chong,et al.  Epigenetic germline inheritance. , 2004, Current opinion in genetics & development.

[6]  S. Henikoff,et al.  Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription , 2007, Nature Genetics.

[7]  R. Feil,et al.  Environmental and nutritional effects on the epigenetic regulation of genes. , 2006, Mutation research.

[8]  J. Sedat,et al.  The absence of detectable methylated bases in Drosophila melanogaster DNA , 1982, FEBS letters.

[9]  S. Clark,et al.  High sensitivity mapping of methylated cytosines. , 1994, Nucleic acids research.

[10]  L. Field,et al.  DNA methylation in insects , 2004, Insect molecular biology.

[11]  M. Labra,et al.  Specific hypomethylation of DNA is induced by heavy metals in white clover and industrial hemp , 2004 .

[12]  Yi Zhang.  Transcriptional regulation by histone ubiquitination and deubiquitination. , 2003, Genes & development.

[13]  A. Bird.  DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[14]  M W Simmen,et al.  Nonmethylated transposable elements and methylated genes in a chordate genome. , 1999, Science.

[15]  L. Field.  Methylation and expression of amplified esterase genes in the aphid Myzus persicae (Sulzer). , 2000, The Biochemical journal.

[16]  John Quackenbush,et al.  TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets , 2003, Bioinform..

[17]  Colin R. Janssen,et al.  Multi-generation cadmium acclimation and tolerance in Daphnia magna Straus. , 2004, Environmental pollution.

[18]  R. Durbin,et al.  The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics , 2003, PLoS biology.

[19]  J. R. Morris,et al.  Genes, genetics, and epigenetics: a correspondence. , 2001, Science.

[20]  W. Ji,et al.  Global DNA hypomethylation, rather than reactive oxygen species (ROS), a potential facilitator of cadmium-stimulated K562 cell proliferation. , 2008, Toxicology letters.

[21]  M. Peinado,et al.  Methylome profiling of cancer cells by amplification of inter-methylated sites (AIMS). , 2002, Nucleic acids research.

[22]  M. Waalkes,et al.  Effects of cadmium on DNA-(Cytosine-5) methyltransferase activity and DNA methylation status during cadmium-induced cellular transformation. , 2003, Experimental cell research.

[23]  C. Naughton,et al.  Epigenetic Transgenerational Actions of Endocrine Disruptors and Male Fertility , 2006 .

[24]  Adrian Bird,et al.  CpG methylation is targeted to transcription units in an invertebrate genome. , 2007, Genome research.

[25]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[26]  M. Mandrioli.  A new synthesis in epigenetics: towards a unified function of DNA methylation from invertebrates to vertebrates , 2007, Cellular and Molecular Life Sciences.

[27]  P. Grant,et al.  A tale of histone modifications , 2001, Genome Biology.

[28]  A. Bird,et al.  Gene number, noise reduction and biological complexity. , 1995, Trends in genetics : TIG.

[29]  R. Watson,et al.  Epigenetics and DNA methylation come of age in toxicology. , 2002, Toxicological sciences : an official journal of the Society of Toxicology.

[30]  H. Birnboim,et al.  A rapid alkaline extraction procedure for screening recombinant plasmid DNA. , 1979, Nucleic acids research.

[31]  A. Warner,et al.  Absence of detectable 5-methylcytosine in DNA of embryos of the brine shrimp, Artemia. , 1984, Developmental biology.

[32]  F. Lyko,et al.  DNA methylation learns to fly. , 2001, Trends in genetics : TIG.

[33]  H. F. Carvalho,et al.  The prima donna of epigenetics: the regulation of gene expression by DNA methylation. , 2005, Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas.

[34]  T. Bestor,et al.  Eukaryotic cytosine methyltransferases. , 2005, Annual review of biochemistry.

[35]  S Tweedie,et al.  Methylation of genomes and genes at the invertebrate-vertebrate boundary , 1997, Molecular and cellular biology.

[36]  M. Szyf,et al.  The dynamic epigenome and its implications in toxicology. , 2007, Toxicological sciences : an official journal of the Society of Toxicology.

[37]  E. Oakeley.  DNA methylation analysis: a review of current methodologies. , 1999, Pharmacology & therapeutics.

[38]  R. Jaenisch,et al.  Development: DNA methylation in Drosophila melanogaster , 2000, Nature.

[39]  B.-P. Elendt,et al.  Trace nutrient deficiency in Daphnia magna cultured in standard medium for toxicity testing. Effects of the optimization of culture conditions on life history parameters of D. magna , 1990 .

[40]  E. Lander,et al.  The Mammalian Epigenome , 2007, Cell.

[41]  Shizhen Song,et al.  Effects of long-term low-dose cadmium exposure on genomic DNA methylation in human embryo lung fibroblast cells. , 2008, Toxicology.

[42]  Robert A. Waterland,et al.  Transposable Elements: Targets for Early Nutritional Effects on Epigenetic Gene Regulation , 2003, Molecular and Cellular Biology.

[43]  G. Robinson,et al.  Functional CpG Methylation System in a Social Insect , 2006, Science.