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.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $20.83 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Gene Expression Omnibus
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).
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).
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).
Field, L.M. Methylation and expression of amplified esterase genes in the aphid Myzus persicae (Sulzer). Biochem. J. 349, 863–868 (2000).
Wang, Y. et al. Functional CpG methylation system in a social insect. Science 314, 645–647 (2006).
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).
Xiang, Z. Genetics and Breeding of the Silkworm (Chinese Agriculture Press, Beijing, P.R. China, 1995).
Kalisz, S. & Purugganan, M.D. Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol. Evol. 19, 309–314 (2004).
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).
Schaefer, M. & Lyko, F. DNA methylation with a sting: an active DNA methylation system in the honeybee. Bioessays 29, 208–211 (2007).
Uno, T. et al. Expression, purification and characterization of methyl DNA binding protein from Bombyx mori. J. Insect Sci. 5, 8 (2005).
Xia, Q. et al. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306, 1937–1940 (2004).
Suzuki, M.M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet. 9, 465–476 (2008).
Mandrioli, M. & Borsatti, F. DNA methylation of fly genes and transposons. Cell. Mol. Life Sci. 63, 1933–1936 (2006).
Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).
Zhang, X. The epigenetic landscape of plants. Science 320, 489–492 (2008).
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).
Lawrence, R.J. & Pikaard, C.S. Chromatin turn ons and turn offs of ribosomal RNA genes. Cell Cycle 3, 880–883 (2004).
Mandrioli, M. & Borsatti, F. Analysis of heterochromatic epigenetic markers in the holocentric chromosomes of the aphid Acyrthosiphon pisum. Chromosome Res. 15, 1015–1022 (2007).
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).
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).
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).
Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189–1201 (2006).
Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).
Ye, J. et al. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 34, W293–297 (2006).
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).
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).
Li, R. et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25, 1966–1967 (2009).
Li, R., Li, Y., Kristiansen, K. & Wang, J. SOAP: short oligonucleotide alignment program. Bioinformatics 24, 713–714 (2008).
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.
The authors declare no competing financial interests.
About this article
DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori
BMC Genomics (2019)
Comparative mitochondrial genomes provide new insights into the true wild progenitor and origin of domestic silkworm Bombyx mori
International Journal of Biological Macromolecules (2019)
Changes in gene DNA methylation and expression networks accompany caste specialization and age‐related physiological changes in a social insect
Molecular Ecology (2019)
Implication for DNA methylation involved in the host transfer of diamondback moth, Plutella xylostella (L.)
Archives of Insect Biochemistry and Physiology (2019)
High-resolution DNA methylome reveals that demethylation enhances adaptability to continuous cropping comprehensive stress in soybean
BMC Plant Biology (2019)