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

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  • An Erratum to this article was published on 01 July 2010

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.

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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.

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  • 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.

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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

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.

Correspondence to Qingyou Xia or Wen Wang or Jun Wang.

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The authors declare no competing financial interests.

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