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

Hui Xiang; Jingde Zhu; Quan Chen; Fangyin Dai; Xin Li; Muwang Li; Hongyu Zhang; Guojie Zhang; Dong Li; Yang Dong; Li Zhao; Ying Lin; Daojun Cheng; Jian Yu; Jinfeng Sun; Xiaoyu Zhou; Kelong Ma; Yinghua He; Yangxing Zhao; Shicheng Guo; Mingzhi Ye; Guangwu Guo; Yingrui Li; Ruiqiang Li; Xiuqing Zhang; Lijia Ma; Karsten Kristiansen; Qiuhong Guo; Jianhao Jiang; Stephan Beck; Qingyou Xia; Wen Wang; Jun Wang

doi:10.1038/nbt.1626

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

Hui Xiang, Jingde Zhu, Quan Chen, Fangyin Dai, Xin Li, Muwang Li, Hongyu Zhang, Guojie Zhang, Dong Li, Yang Dong, Li Zhao, Ying Lin, Daojun Cheng, Jian Yu, Jinfeng Sun, Xiaoyu Zhou, Kelong Ma, Yinghua He, Yangxing Zhao, Shicheng GuoMingzhi Ye, Guangwu Guo, Yingrui Li, Ruiqiang Li, Xiuqing Zhang, Lijia Ma, Karsten Kristiansen, Qiuhong Guo, Jianhao Jiang, Stephan Beck, Qingyou Xia, Wen Wang, Jun Wang

Department of Biology

213 Citations (Scopus)

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.

Original language	English
Journal	Nature Biotechnology
Volume	28
Issue number	5
Pages (from-to)	516-20
Number of pages	4
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt.1626
Publication status	Published - May 2010

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Xiang, H, Zhu, J, Chen, Q, Dai, F, Li, X, Li, M, Zhang, H, Zhang, G, Li, D, Dong, Y, Zhao, L, Lin, Y, Cheng, D, Yu, J, Sun, J, Zhou, X, Ma, K, He, Y, Zhao, Y, Guo, S, Ye, M, Guo, G, Li, Y, Li, R, Zhang, X, Ma, L, Kristiansen, K, Guo, Q, Jiang, J, Beck, S, Xia, Q, Wang, W & Wang, J 2010, 'Single base-resolution methylome of the silkworm reveals a sparse epigenomic map', Nature Biotechnology, vol. 28, no. 5, pp. 516-20. https://doi.org/10.1038/nbt.1626

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title = "Single base-resolution methylome of the silkworm reveals a sparse epigenomic map",

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.",

author = "Hui Xiang and Jingde Zhu and Quan Chen and Fangyin Dai and Xin Li and Muwang Li and Hongyu Zhang and Guojie Zhang and Dong Li and Yang Dong and Li Zhao and Ying Lin and Daojun Cheng and Jian Yu and Jinfeng Sun and Xiaoyu Zhou and Kelong Ma and Yinghua He and Yangxing Zhao and Shicheng Guo and Mingzhi Ye and Guangwu Guo and Yingrui Li and Ruiqiang Li and Xiuqing Zhang and Lijia Ma and Karsten Kristiansen and Qiuhong Guo and Jianhao Jiang and Stephan Beck and Qingyou Xia and Wen Wang and Jun Wang",

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AU - Xiang, Hui

AU - Zhu, Jingde

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AU - Li, Xin

AU - Li, Muwang

AU - Zhang, Hongyu

AU - Zhang, Guojie

AU - Li, Dong

AU - Dong, Yang

AU - Zhao, Li

AU - Lin, Ying

AU - Cheng, Daojun

AU - Yu, Jian

AU - Sun, Jinfeng

AU - Zhou, Xiaoyu

AU - Ma, Kelong

AU - He, Yinghua

AU - Zhao, Yangxing

AU - Guo, Shicheng

AU - Ye, Mingzhi

AU - Guo, Guangwu

AU - Li, Yingrui

AU - Li, Ruiqiang

AU - Zhang, Xiuqing

AU - Ma, Lijia

AU - Kristiansen, Karsten

AU - Guo, Qiuhong

AU - Jiang, Jianhao

AU - Beck, Stephan

AU - Xia, Qingyou

AU - Wang, Wen

AU - Wang, Jun

PY - 2010/5

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N2 - 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.

AB - 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.

U2 - 10.1038/nbt.1626

DO - 10.1038/nbt.1626

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C2 - 20436463

SN - 1087-0156

VL - 28

SP - 516

EP - 520

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 5

ER -

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

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