| Single base-resolution methylome of the silkworm reveals a sparse epigenomic map | |
| Xiang H1,2; Zhu JD3,4; Chen Q2; Dai FY5; Li X1; Li MW6; Zhang HY3; Zhang GJ2; Li D5; Dong Y1; Wang W*1; Wang J*2,7; Xia QY*5; xiaqy@swu.edu.cn; wwang@mail.kiz.ac.cn; wangj@genomics.org.cn | |
| 2010 | |
| 发表期刊 | NATURE BIOTECHNOLOGY
 |
| ISSN | 1087-0156 |
| 卷号 | 28期号:5页码:516-U181 |
| 合作性质 | 其它 |
| 摘要 | 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 Arabidopsis(1) and human(2), demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation. |
| 资助者 | 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. ; 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. ; 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. ; 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. |
| 收录类别 | SCI |
| 语种 | 英语 |
| 资助者 | 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. ; 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. ; 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. ; 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. |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.kiz.ac.cn/handle/152453/4857 |
| 专题 | 基因起源组 遗传资源与进化国家重点实验室 |
| 通讯作者 | xiaqy@swu.edu.cn; wwang@mail.kiz.ac.cn; wangj@genomics.org.cn |
| 作者单位 | 1.CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, China 2.BGI-Shenzhen, Shenzhen, China 3.Cancer Epigenetics and Gene Therapy Program, The State-key Laboratory for Oncogenes and Related Genes, Shanghai Cancer Institute, Shanghai Jiaotong University, Shanghai, China 4.Cancer Epigenetics Laboratory, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China 5.The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China 6.Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China 7.Department of Biology, University of Copenhagen, Denmark 8.Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai, China 9.UCL Cancer Institute, University College London, London, UK |
| 推荐引用方式 GB/T 7714 | Xiang H,Zhu JD,Chen Q,et al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map[J]. NATURE BIOTECHNOLOGY,2010,28(5):516-U181. |
| APA | Xiang H.,Zhu JD.,Chen Q.,Dai FY.,Li X.,...&wangj@genomics.org.cn.(2010).Single base-resolution methylome of the silkworm reveals a sparse epigenomic map.NATURE BIOTECHNOLOGY,28(5),516-U181. |
| MLA | Xiang H,et al."Single base-resolution methylome of the silkworm reveals a sparse epigenomic map".NATURE BIOTECHNOLOGY 28.5(2010):516-U181. |
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