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First evidence of methylation in the genome of Drosophila willistoni

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Abstract

DNA methylation has been studied abundantly in vertebrates and recent evidence confirms that this phenomenon could be disseminated among some invertebrates groups, including Drosophila species. In this paper, we used the Methylation-Sensitive Restriction Endonuclease (MSRE) technique and Southern blot with specific probes, to detect methylation in the Drosophila willistoni species. We found differential cleavage patterns between males and females that cannot be explained by Mendelian inheritance, pointing to a DNA methylation phenomenon different from the Drosophila melanogaster one. The sequencing of some of these bands showed that these fragments were formed by different DNA elements, among which rDNA. We also characterized the D. willitoni dDnmt2 sequence, through a Mega Blast search against the D. willistoni Trace Archive Database using the D. melanogaster dDnmt2 nucleotide sequence as query. The complete analysis of D. willistoni dDnmt2 sequence showed that its promoter region is larger, its dDnmt2 nucleotide sequence is 33% divergent from the D. melanogaster one, Inverted Terminal Repeats (ITRs) are absent and only the B isoform of the enzyme is produced. In contrast, ORF2 is more conserved. Comparing the D. willistoni and D. melanogaster dDnmt2 protein sequences, we found higher conservation in motifs from the large domain, responsible for the catalysis of methyl transfer, and great variability in the region that carries out the recognition of specific DNA sequences (TRD). Globally, our results reveal that methylation of the D. willistoni genome could be involved in a singular process of species-specific dosage compensation and that the DNA methylation in the Drosophila genus can have diverse functions. This could be related to the evolutionary history of each species and also to the acquisition time of the dDnmt2 gene.

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References

  • Avner P, Heard E (2001) X-chromosome inactivation: counting, choice and initiation. Nat Rev Genet 2: 59–67

    Article  PubMed  CAS  Google Scholar 

  • Baylin SB, Esteller M, Rountree MR, et al. (2001) Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer. Hum Mol Genet 10(7): 687–692

    Article  PubMed  CAS  Google Scholar 

  • Bernstein E, Allis CD (2005) RNA meets chromatin. Genes Dev 19: 1635–1655

    Article  PubMed  CAS  Google Scholar 

  • Bestor TH (2000) The DNA methyltransferases of mammals. Hum Mol Gen 9(16): 2395–2402

    Article  PubMed  CAS  Google Scholar 

  • Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16(1): 6–21

    Article  PubMed  CAS  Google Scholar 

  • Bongiorni S, Cintio O, Prantera G (1999) The relationship between DNA methylation and chromosome imprinting in the Coccid Planococcus citri. Genetics 151: 1471–1478

    PubMed  CAS  Google Scholar 

  • Busslinger M, Hurst J, Flavell RA (1983) DNA methylation and the regulation of globin gene expression. Cell 34: 197–206

    Article  PubMed  CAS  Google Scholar 

  • Colot V, Rossignol JL (1999) Eukaryotic DNA methylation as an evolutionary device. Bioessays 21: 402–411

    Article  PubMed  CAS  Google Scholar 

  • Dahl C, Guldberg P (2003). DNA methylation analysis techniques. Biogerontology 4: 233–250

    Article  PubMed  CAS  Google Scholar 

  • Dong A, Yoder JA, Zhang X, et al. (2001). Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistent binding to DNA. Nucleic Acids Res 29(2): 439–448

    Article  PubMed  CAS  Google Scholar 

  • Ehrlich M, Jackson K, Weemaes C (2006). Immunodeficiency, centromeric region instability, facial anomalies syndrome (ICF). Orphanet J Rare Dis 1: 1–2

    Article  Google Scholar 

  • Field LM (2000) Methylation and expression of amplified esterase genes in the aphid Myzus persicae (Sulzer). Biochem J 349: 863–868

    PubMed  CAS  Google Scholar 

  • Field LM, Devonshire AL, French-Constant RH, et al. (1989) Changes in DNA methylation are associated with loss of insecticide resistence in the peach-potato aphid Myzus persicae (Sulz.). FEBS Lett. 243: 323–327

    Article  CAS  Google Scholar 

  • Field LM, Lyko F, Mandrioli M, et al. (2004) DNA methylation in insects. Insect Mol Biol 13(2): 109–115

    Article  PubMed  CAS  Google Scholar 

  • Fisher O, Siman-Tov R, Ankri S (2004) Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica. Nucleic Acids Res 32(1): 287–297

    Article  PubMed  CAS  Google Scholar 

  • Ghoshal K, Majumder S, Datta J, et al. (2004) Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression. J Biol Chem 279:6783–6793

    Article  PubMed  CAS  Google Scholar 

  • Gilfillan GD, Dahlsveen IK, Becker PB (2004) Lifting a chromosome: dosage compensation in Drosophila melanogaster. FEBS Lett 567: 8–14

    Article  PubMed  CAS  Google Scholar 

  • Gruenbaum Y, Stein R, Cedar H, et al. (1981) Methylation of CpG sequences in eukariotic DNA. FEBS Lett 124: 67–71

    Article  PubMed  CAS  Google Scholar 

  • Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95–98

    CAS  Google Scholar 

  • Heard E (2004) Recent advances in X-chromosome inactivation. Curr Opin Cell Biol 16: 247–255

    Article  PubMed  CAS  Google Scholar 

  • Hick CA, Field LM, Devonshire AL (1996) Changes in the methylation of amplified esterase DNA during loss and reselection of insecticide resistence in peach-potato aphids, Myzus persicae. Insect Biochem Mol Biol 26: 41–47

    Article  PubMed  CAS  Google Scholar 

  • Higgins DG, Bleasby AJ, Fuchs R (1994) Clustal W: improved software for multiple sequence alignment. Computer applications in the Bioscience. CABIOS 8: 189–191

    Google Scholar 

  • Jowett T (1986) Preparation of nucleic acids. In: Roberts DB (ed). Drosophila: a practical approach. IRL Press, Oxford

    Google Scholar 

  • Kumar S, Cheng X, Klimasauskas S, et al. (1994) The DNA (cytosine-5) methyltransferases. Nucleic Acids Res 22(1): 1–10

    Article  PubMed  CAS  Google Scholar 

  • Kunert N, Marhold J, Stanke J, et al. (2003). A Dnmt2-like protein mediates DNA methylation in Drosophila. Development 130: 5083–5090

    Article  PubMed  CAS  Google Scholar 

  • Li E, Bestor TH, Jaenisch R (1992) Targed mutation of the DNA methyltranferase gene results in embryonic lethality. Cell 69: 915–926

    Article  PubMed  CAS  Google Scholar 

  • Lloyd V. (2000) Parental imprinting in Drosophila. Genetica 109: 35–44

    Article  PubMed  CAS  Google Scholar 

  • Lyko F (2001) DNA methylation learns to fly. Trends Genet 17(4): 169–172

    Article  PubMed  CAS  Google Scholar 

  • Lyko F, Beisel C, Marhold J, et al. (2006) Epigenetic regulation in Drosophila. Curr Trop Microbiol Immunol 310: 23–44

    CAS  Google Scholar 

  • Lyko F, Ramsahoye BH, Jaenisch R (2000) DNA methylation in Drosophila melanogaster. Nature 408(30): 538–540

    PubMed  CAS  Google Scholar 

  • Mandrioli M, Volpi N (2003) The genome of the lepidopteran Mamestra brassicae has a vertebrate-like content of methyl-cytosine. Genetica 119: 187–191

    Article  PubMed  CAS  Google Scholar 

  • Marhold J, Rothe N, Pauli A (2004) Conservation of methylation in dipteran insects. Insect Mol Biol 13(2): 117–123

    Article  PubMed  CAS  Google Scholar 

  • Marques EK, Napp M, Winge H (1966) A corn meal, soybean fluor, wheat germ medium for Drosophila. Drosoph Inf Serv 41: 187

    Google Scholar 

  • Nicholas KB, Nicholas HB Jr, Deerfield DW II (1997) GeneDoc: analysis and visualization of genetic variation EMBNEW. NEWS 4:1–4

    Google Scholar 

  • Norris DP, Patel D, Kay GF, et al. (1994) Evidence that random and imprinted Xist expression is controlled by preemptive methylation. Cell 77: 41–51

    Article  PubMed  CAS  Google Scholar 

  • Nur U (1990) Heterochromatinization and euchromatinization of whole genomes in scale insects (Coccoidea: Homoptera). Development Suppl: 29–34

  • Okano M, Bell DW, Haber DA, et al. (1999) DNA methyltransferasesDnmt3a and Dnmt3b are assential for de novo methylation and mammalian development. Cell 99: 247–257

    Article  PubMed  CAS  Google Scholar 

  • Okano M, Xie S, Li E (1998) Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells. Nucleic Acids Res 26: 2536–2540

    Article  PubMed  CAS  Google Scholar 

  • Paz MF, Fraga MF, Ávila S, et al. (2003) A systematic profile of DNA methylation in human cancer cell lines. Cancer Res 63(5): 1114–1121

    PubMed  CAS  Google Scholar 

  • Ponger L, Li W (2005) Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol Biol Evol 22(4): 1119–1128

    Article  PubMed  CAS  Google Scholar 

  • Riggs AD (1975) X inativation, differentiation, and DNA metylation. Cytogenet Cell Genet 14: 9–25

    PubMed  CAS  Google Scholar 

  • Russo VEA, Martienssen RA, Riggs AD (1996) Epigenetic mechanisms of gene regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Santoro R, Grummt I (2001) Molecular mechanisms mediating methylation-dependent silencing of ribosomal gene transcription. Mol Cell 8: 719–725

    Article  PubMed  CAS  Google Scholar 

  • Santoro R, Grummt I (2005) Epigenetic mechanism of rDNA gene silencing: temporal order of NoRC-mediated histone modification, chromatin remodelling, and DNA methylation. Mol Cell Biol 25: 2539–2546

    Article  PubMed  CAS  Google Scholar 

  • Scarbrough K, Hattman S, Nur U (1984) Relationship of DNA methylation level to the presence of heterochromatin on mealybugs. Mol Cell Biol 4: 599–603

    PubMed  CAS  Google Scholar 

  • Shiota K, Kogo Y, Ohgane J (2002). Epigenetic marks by DNA methylation specific to stem germ and somatic cells in mice. Genes Cells 7(9):961–969

    Article  PubMed  CAS  Google Scholar 

  • Staden R (1996) The Staden sequence analysis package. Mol Biotechnol 5(3): 233–241

    Article  PubMed  CAS  Google Scholar 

  • Straub T, Dahlsveen IK, Becker PB (2005) Dosage compensation in flies: mechanism, models, mystery. FEBS Lett 579: 3258–3263

    Article  PubMed  CAS  Google Scholar 

  • Tang L, Reddy MN, Rasheva V, et al. (2003) The eukaryotic DNMT2 genes encode a new class of cytosine-5 DNA methyltransferases. J. Biol. Chem. 278(36): 33613–33616

    Article  PubMed  CAS  Google Scholar 

  • Tautz D, Hancock J, Webb D, et al. (1988) Complete sequences of the rRNA genes of Drosophila melanogaster. Mol Biol Evol 5: 366–376

    PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Tweedie S, Charlton J, Clarck V, et al. (1997) Methylation of genomes and genes at the invertebrate-vertebrate boundary. Mol Cell Biol 17: 1469–1475

    PubMed  CAS  Google Scholar 

  • Urieli-Shoval S, Gruenbaum Y, Sedat J, et al. (1982) The absence of detectable methylated bases in Drosophila melanogaster DNA. FEBS Lett 146(1): 148–152

    Article  PubMed  CAS  Google Scholar 

  • Wade PA (2001) Methyl CpG binding proteins: coupling chromatin architecture to gene regulation. Oncogene 20: 3166–3173

    Article  PubMed  CAS  Google Scholar 

  • Weinhold B (2006) Epigenetics: the science of change. Environ Health Perspect 114(3): A160–167

    Article  PubMed  Google Scholar 

  • Yoder JA, Soman NS, Verdine GL, et al. (1997) DNA(cytosine-5)-methyltransferase in mouse cells and tissues. Studies with a mechanism-based probe. J Mol Biol 270: 385–395

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

To CNPq, FAPERGS and PROPESQ-UFRGS for fellowships and grants; to Dr. Carlos Polanco de la Puente (University of Leicester) for supplying rDNA probe. To Dr. Henrique B. Ferreira (Cestódeos Molecular Biology Laboratory, UFRGS) for support the cloning process. We thank Dr. Wolfgang J. Miller (Laboratories of Genome Dynamics Center of Anatomy and Cell Biology, Vienna, Austria) for comments on the manuscript.

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Authors and Affiliations

  1. Programa de Pós Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, CEP 91501-970, Porto Alegre, RS, Brazil

    Rosane Nunes Garcia

  2. Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, CEP 91501-970, Porto Alegre, RS, Brazil

    Rosane Nunes Garcia, Marícia Fantinel D’Ávila, Lizandra Jaqueline Robe, Fabiana Oliveira de Heredia & Vera Lúcia da Silva Valente

  3. Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil

    Elgion Lúcio da Silva Loreto

  4. Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay

    Yanina Panzera

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  1. Rosane Nunes Garcia
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Correspondence to Rosane Nunes Garcia.

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Garcia, R.N., D’Ávila, M.F., Robe, L.J. et al. First evidence of methylation in the genome of Drosophila willistoni . Genetica 131, 91–105 (2007). https://doi.org/10.1007/s10709-006-9116-3

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