Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

An Erratum to this article was published on 01 July 2010

This article has been updated

Abstract

Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic cytosines are methylcytosines, all of which probably occur in CG dinucleotides. CG methylation is substantially enriched in gene bodies and is positively correlated with gene expression levels, suggesting it has a positive role in gene transcription. We find that transposable elements, promoters and ribosomal DNAs are hypomethylated, but in contrast, genomic loci matching small RNAs in gene bodies are densely methylated. This work contributes to our understanding of epigenetics in insects, and in contrast to previous studies of the highly methylated genomes of Arabidopsis1 and human2, demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: DNA methylation patterns and chromosomal distribution in Bombyx mori.
Figure 2: Methylation of different functional regions of Bombyx mori (Dazao).
Figure 3: Relationship between DNA methylation and expression levels of genes in Bombyx mori (Dazao).
Figure 4: Annotation and microarray analysis of methylated and unmethylated genes.

Similar content being viewed by others

Accession codes

Accessions

Gene Expression Omnibus

Change history

  • 09 July 2010

    In the version of this article initially published, references 4 and 7 were inadvertently interchanged. The error has been corrected in the HTML and PDF versions of the article.

References

  1. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).

    Article  CAS  Google Scholar 

  2. Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).

    Article  CAS  Google Scholar 

  3. Regev, A., Lamb, J.M. & Jablonka, E. The role of DNA methylation in invertebrates: developmental regulation or genome defense? Mol. Biol. Evol. 15, 880–891 (1998).

    Article  CAS  Google Scholar 

  4. Patel, C.V. & Gopinathan, K.P. Determination of trace amounts of 5-methylcytosine in DNA by reverse-phase high-performance liquid chromatography. Anal. Biochem. 164, 164–169 (1987).

    Article  CAS  Google Scholar 

  5. Field, L.M. Methylation and expression of amplified esterase genes in the aphid Myzus persicae (Sulzer). Biochem. J. 349, 863–868 (2000).

    Article  CAS  Google Scholar 

  6. Wang, Y. et al. Functional CpG methylation system in a social insect. Science 314, 645–647 (2006).

    Article  CAS  Google Scholar 

  7. Phalke, S. et al. Retrotransposon silencing and telomere integrity in somatic cells of Drosophila depends on the cytosine-5 methyltransferase DNMT2. Nat. Genet. 41, 696–702 (2009).

    Article  CAS  Google Scholar 

  8. Xiang, Z. Genetics and Breeding of the Silkworm (Chinese Agriculture Press, Beijing, P.R. China, 1995).

  9. Kalisz, S. & Purugganan, M.D. Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol. Evol. 19, 309–314 (2004).

    Article  Google Scholar 

  10. Farcas, R. et al. Differences in DNA methylation patterns and expression of the CCRK gene in human and nonhuman primate cortices. Mol. Biol. Evol. 26, 1379–1389 (2009).

    Article  CAS  Google Scholar 

  11. Schaefer, M. & Lyko, F. DNA methylation with a sting: an active DNA methylation system in the honeybee. Bioessays 29, 208–211 (2007).

    Article  CAS  Google Scholar 

  12. Uno, T. et al. Expression, purification and characterization of methyl DNA binding protein from Bombyx mori. J. Insect Sci. 5, 8 (2005).

    PubMed  PubMed Central  Google Scholar 

  13. Xia, Q. et al. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306, 1937–1940 (2004).

    Article  Google Scholar 

  14. Suzuki, M.M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9, 465–476 (2008).

    Article  CAS  Google Scholar 

  15. Mandrioli, M. & Borsatti, F. DNA methylation of fly genes and transposons. Cell. Mol. Life Sci. 63, 1933–1936 (2006).

    Article  CAS  Google Scholar 

  16. Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).

    Article  CAS  Google Scholar 

  17. Zhang, X. The epigenetic landscape of plants. Science 320, 489–492 (2008).

    Article  CAS  Google Scholar 

  18. Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T. & Henikoff, S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39, 61–69 (2007).

    Article  CAS  Google Scholar 

  19. Lawrence, R.J. & Pikaard, C.S. Chromatin turn ons and turn offs of ribosomal RNA genes. Cell Cycle 3, 880–883 (2004).

    Article  CAS  Google Scholar 

  20. Mandrioli, M. & Borsatti, F. Analysis of heterochromatic epigenetic markers in the holocentric chromosomes of the aphid Acyrthosiphon pisum. Chromosome Res. 15, 1015–1022 (2007).

    Article  CAS  Google Scholar 

  21. Elango, N., Kim, S.H., Vigoda, E. & Yi, S.V. Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation. PLOS Comput. Biol. 4, e1000015 (2008).

    Article  Google Scholar 

  22. Elango, N., Hunt, B.G., Goodisman, M.A. & Yi, S.V. DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera. Proc. Natl. Acad. Sci. USA 106, 11206–11211 (2009).

    Article  CAS  Google Scholar 

  23. Suzuki, M.M., Kerr, A.R., De Sousa, D. & Bird, A. CpG methylation is targeted to transcription units in an invertebrate genome. Genome Res. 17, 625–631 (2007).

    Article  CAS  Google Scholar 

  24. Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201 (2006).

    Article  CAS  Google Scholar 

  25. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).

    Article  CAS  Google Scholar 

  26. Ye, J. et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 34, W293–297 (2006).

    Article  CAS  Google Scholar 

  27. Liao, B.Y. & Zhang, J. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol. Biol. Evol. 23, 1119–1128 (2006).

    Article  CAS  Google Scholar 

  28. Hayatsu, H., Tsuji, K. & Negishi, K. Does urea promote the bisulfite-mediated deamination of cytosine in DNA? Investigation aiming at speeding-up the procedure for DNA methylation analysis. Nucleic Acids Symp. Ser. 50, 69–70 (2006).

    Article  Google Scholar 

  29. Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966–1967 (2009).

    Article  CAS  Google Scholar 

  30. Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714 (2008).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Ridley for English editing on the manuscript. This work was supported by a 973 Program grant (no. 2007CB815700), a key project of the National Natural Science Foundation of China (no. 90919056), the 100 Talents Program of Chinese Academy of Sciences, two Provincial Key Grants of the Department of Sciences and Technology of Yunnan Province (no. 2008CC017 and no. 2008GA002) and a Chinese Academy of Sciences–Max Planck Society Fellowship to W.W.; a National Natural Science Foundation of China grant (no. 30870296) and a China Postdoctoral Science Foundation grant to H.X.; the National Natural Science Foundation of China (no. 30725008), a Chinese 863 Program grant (no. 2006AA10A121), the Danish Platform for Integrative Biology, the Ole Rømer grant from the Danish Natural Science Research Council, and a Solexa Project grant (no. 272-07-0196) to J.W.; a 973 Program grant (no. 2005CB121000) to Q.X.; a Shanghai Science Foundation grant (no. 07DJ14074), two National Science Foundation grants (no. 90919024 and no. 30872963), two 973 Program grants (no. 2009CB825606 and no. 2009CB825607) and a European 6th program grant (no. LSHB-CT-2005-019067) to J.Z.

Author information

Authors and Affiliations

Authors

Contributions

J.W., W.W., J.Z. and Q.X. designed the study. H.X., W.W. and X.L. wrote the manuscript. X.L., G.Z., Q.C., Y.L. and R.L. developed the method for mapping and processing BS reads. D.L. and D.C., performed microarray analysis. F.D. and M.L. provided the domestic silkworm samples and detailed background information on silkworm domestication and breeding. H.X. and X.L. analyzed the 454 data. H.X. did RT-PCR. Y.D. performed the methyltransferase assay. H.X., Y.L., Q.G. and J.J. extracted DNAs and RNAs. J.Z., H.Z., J.Y., J.S., X.Z., K.M., L.Z., Y.H., S.G. and Y.Z. constructed the BS-seq libraries and conducted the BS validation. G.G., X.Z., L.M., M.Y. and K.K. performed the Solexa sequencing. S.B. contributed to the interpretation of the results. All authors have read and contributed to the manuscript.

Corresponding authors

Correspondence to Qingyou Xia, Wen Wang or Jun Wang.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–4 and Figures 1–5 (PDF 867 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Xiang, H., Zhu, J., Chen, Q. et al. Single base–resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 28, 516–520 (2010). https://doi.org/10.1038/nbt.1626

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt.1626

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing