Single base-resolution methylome of the silkworm reveals a sparse epigenomic map.
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 and human, demonstrates a strategy for sequencing the epigenomes of organisms such as insects that have low levels of methylation.
Xiang
Hui
H
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.
Zhu
Jingde
J
Chen
Quan
Q
Dai
Fangyin
F
Li
Xin
X
Li
Muwang
M
Zhang
Hongyu
H
Zhang
Guojie
G
Li
Dong
D
Dong
Yang
Y
Zhao
Li
L
Lin
Ying
Y
Cheng
Daojun
D
Yu
Jian
J
Sun
Jinfeng
J
Zhou
Xiaoyu
X
Ma
Kelong
K
He
Yinghua
Y
Zhao
Yangxing
Y
Guo
Shicheng
S
Ye
Mingzhi
M
Guo
Guangwu
G
Li
Yingrui
Y
Li
Ruiqiang
R
Zhang
Xiuqing
X
Ma
Lijia
L
Kristiansen
Karsten
K
Guo
Qiuhong
Q
Jiang
Jianhao
J
Beck
Stephan
S
Xia
Qingyou
Q
Wang
Wen
W
Wang
Jun
J
D000818:Animals; D012831:Bombyx / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D049750:Genome, Insect; D017422:Sequence Analysis, DNA