Journal of Molecular Evolution

, Volume 68, Issue 6, pp 700–705 | Cite as

In Silico Prediction of Two Classes of Honeybee Genes with CpG Deficiency or CpG Enrichment and Sorting According to Gene Ontology Classes



Two honeybee DNA methyltransferase genes have recently been identified and confirmed to be functional. The honeybee genes under regulation by DNA methylation may therefore be CpG deficient, due to natural deamination of methylated DNA. In this report, we show that <39% of the known honeybee genes are likely to be methylated on the basis of their low CpG obs/exp ratios. In contrast, orthologues of these genes in the fruitfly do not show CpG deficiency. Classes of function as determined by Gene Ontology were obtained for the honeybee genes with significantly low and high CpG obs/exp ratios. Overrepresented classes in the low CpG[obs/exp] genes are involved in transcription, translation, protein folding, protein localization, protein transportation, cell cycle, and DNA and RNA metabolism.


Honeybee DNA methylation Gene Ontology classes CpG deficiency 



We thank two anonymous reviewers for helpful comments. We are grateful to Dr. Michael Santos and Dr. Shawn Arellano for critical reading of the manuscript.

Supplementary material

239_2009_9244_MOESM1_ESM.pdf (191 kb)
MOSESM1 (PDF 190 kb)


  1. Bestor TH (1990) DNA methylation: evolution of a bacterial immune function into a regulator to gene expression and genome structure in higher eukaryotes. Philos Trans R Soc Lond B 326:179–187CrossRefGoogle Scholar
  2. Bird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8:1499–1504PubMedCrossRefGoogle Scholar
  3. Blüthgen N, Brand K, Cajavec B, Swat M, Herzel H, Beule D (2005) Biological profiling of gene groups utilizing Gene Ontology. Genome Inform 16:106–115PubMedGoogle Scholar
  4. Burge C, Campbell AM, Karlin S (1992) Over- and under-representation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci USA 89:1358–1362PubMedCrossRefGoogle Scholar
  5. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676PubMedCrossRefGoogle Scholar
  6. Cooper DN, Youssoufian H (1988) The CpG dinucleotide and human genetic disease. Hum Genet 78:151–155PubMedCrossRefGoogle Scholar
  7. Coulonder C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775–780CrossRefGoogle Scholar
  8. Duncan BK, Miller JH (1980) Mutagenic deamination of cytosine residues in DNA. Nature 287:560–561PubMedCrossRefGoogle Scholar
  9. Gowher H, Leismann O, Jeltsch A (2000) DNA of Drosophila melanogaster contains 5-methylcytosine. EMBO J 19:6918–6923PubMedCrossRefGoogle Scholar
  10. Kucharski R, Maleszka J, Foret S, Maleszka R (2008) Nutrtional control of reproductive status in honeybees via DNA methylation. Science 319:1827–1830PubMedCrossRefGoogle Scholar
  11. Polak P, Arndt PF (2008) Transcription induces strand-specific mutations at the 5′ end of human genes. Genome Res 18:1216–1223PubMedCrossRefGoogle Scholar
  12. Regev A, Lamb MJ, Jablonka E (1998) The role of DNA methylation in invertebrates: developmental regulation or genome defense? Mol Biol Evol 15:880–891Google Scholar
  13. Simmen MW, Leitgeb S, Charlton J, Jones SJM, Harris BR, Clark VH, Bird A (1999) Nonmethylated transposable elements and methylated genes in a chordate genome. Science 283:1164–1167PubMedCrossRefGoogle Scholar
  14. Singer J, Roberts-Ems J, Luthardt FW, Riggs FW (1979) Methylation of DNA in mouse early embryos, teratocarcinoma cells and adult tissues of mouse and rabbit. Nucleic Acids Res 7:2369–2385PubMedCrossRefGoogle Scholar
  15. Suzuki MM, Kerr ARW, Sousa DD, Bird A (2007) CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res 17:625–631PubMedCrossRefGoogle Scholar
  16. The Honeybee Genome Sequencing Consortium (2006) Insights into social insects from the genome of the honeybee Apis mellifera. Nature 443:931–949Google Scholar
  17. Wang Y, Jorda M, Jones PL, Maleszka R, Ling X, Robertson HM, Mizzen CA, Peinado MA, Robinson GE (2006) Functional CpG methylation system in a social insect. Science 314:645–647PubMedCrossRefGoogle Scholar
  18. Yoder JA, Walsh CP, Bestor HT (1997) Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13:335–340PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.School of Biological Sciences and Genome Research CentreThe University of Hong KongPokfulam, Hong KongChina

Personalised recommendations