Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc.
Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc.
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作者：
Gavery MR;Roberts SB
太平洋牡蛎（Crassostrea gigas）DNA甲基化模式的特征表明，这种表观遗传机制在基因调控中起着重要的功能作用，并可能参与发育过程和环境响应的调控。然而，以前的研究仅限于在单基因水平上对DNA甲基化进行计算机分析或表征。在这里，我们采用了全基因组的方法来深入了解DNA甲基化如何支持C.千兆。使用甲基化富集和高通量亚硫酸氢盐测序的组合，我们已经能够在超过250万个单独的CpG基因座上绘制甲基化图谱。这是第一个高分辨率甲基化产生的软体动物物种。结果表明，甲基化在基因组中的空间变化与大多数的甲基化位点映射到基因内区域。将亚硫酸氢盐测序数据与RNA-seq数据相结合，以检查基因体甲基化和基因表达之间的全基因组关系，其中显示甲基化基因与组织类型之间的高转录丰度和低表达变异相关。综合数据表明，DNA甲基化在调控双壳类基因组活性中起着复杂的作用。
Characterization of DNA methylation patterns in the Pacific oyster, Crassostrea gigas, indicates that this epigenetic mechanism plays an important functional role in gene regulation and may be involved in the regulation of developmental processes and environmental responses. However, previous studies have been limited to in silico analyses or characterization of DNA methylation at the single gene level. Here, we have employed a genome-wide approach to gain insight into how DNA methylation supports the regulation of the genome in C. gigas. Using a combination of methylation enrichment and high-throughput bisulfite sequencing, we have been able to map methylation at over 2.5 million individual CpG loci. This is the first high-resolution methylome generated for a molluscan species. Results indicate that methylation varies spatially across the genome with a majority of the methylated sites mapping to intra genic regions. The bisulfite sequencing data was combined with RNA-seq data to examine genome-wide relationships between gene body methylation and gene expression, where it was shown that methylated genes are associated with high transcript abundance and low variation in expression between tissue types. The combined data suggest DNA methylation plays a complex role in regulating genome activity in bivalves.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
3.9
作者：
Huh I;Zeng J;Park T;Yi SV
通讯作者：
Yi SV
寄生线虫旋毛虫离散发育阶段的差异 DNA 甲基化
影响因子：
12.3
作者：
Gao F;Liu X;Wu XP;Wang XL;Gong D;Lu H;Xia Y;Song Y;Wang J;Du J;Liu S;Han X;Tang Y;Yang H;Jin Q;Zhang X;Liu M
通讯作者：
Liu M
影响因子：
3.2
作者：
Fneich S;Dheilly N;Adema C;Rognon A;Reichelt M;Bulla J;Grunau C;Cosseau C
通讯作者：
Cosseau C
影响因子：
64.5
作者：
Okano, M;Bell, DW;Li, E
通讯作者：
Li, E