Data from: Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honey bee genome

Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the GC dinucleotides (CpGs). However, less frequent non-CpG asymmetric methylation has been found in various cell types, such as mammalian neurons, and recent results suggest that these sites can repress transcription independently of CpG contexts. In addition, an emerging view is that hemi-methylation may arise not only from deregulation of cellular processes but also be a standard feature of the methylome. Here we have applied a novel approach to examine if asymmetric cytosine methylation is present in a sparsely methylated genome of the honey bee, a social insect with a high level of epigenetically-driven phenotypic plasticity. By combining strand-specific ultra-deep amplicon sequencing of illustrator genes with whole-genome methylomics and bioinformatics we show that rare asymmetrically methylated cytosines can be unambiguously detected in the honey bee genome. Additionally, we confirm differential methylation between two phenotypically and reproductively distinct castes, queens and workers, and offer new insight into the heterogeneity of brain methylation patterns. In particular, we challenge the assumption that symmetrical methylation levels reflect symmetry in the underlying methylation patterns and conclude that hemimethylation may occur more frequently than indicated by methylation levels. Finally, we question the validity of a prior study in which most of cytosine methylation in this species was reported to be asymmetric.

真核生物的情境依赖性基因表达受多种机制调控，其中以主要发生于GC二核苷酸（CpG）的胞嘧啶甲基化（cytosine methylation）最为关键。不过，在哺乳动物神经元等多种细胞类型中，亦已发现频率较低的非CpG不对称甲基化；近期研究表明，此类位点可独立于CpG背景抑制转录过程。此外，学界新兴观点认为，半甲基化（hemi-methylation）的产生不仅可能源于细胞进程失调，还可作为甲基化组（methylome）的一类标准特征存在。本研究采用全新实验策略，旨在探究在表观遗传驱动下具备高度表型可塑性（phenotypic plasticity）的社会性昆虫——蜜蜂的稀疏甲基化基因组中，是否存在不对称胞嘧啶甲基化。通过结合靶标基因的链特异性超深度扩增子测序（strand-specific ultra-deep amplicon sequencing）、全基因组甲基化组学（whole-genome methylomics）分析与生物信息学（bioinformatics）手段，本研究证实：蜜蜂基因组中可明确检测到罕见的不对称甲基化胞嘧啶位点。此外，本研究验证了两种表型与生殖特征迥异的蜂群品级——蜂王与工蜂之间存在差异化甲基化，并为大脑甲基化模式的异质性提供了全新研究视角。尤为关键的是，我们对“对称甲基化水平可反映其背后甲基化模式的对称性”这一传统假设提出了挑战，并得出结论：半甲基化的发生频率可能高于甲基化水平所提示的程度。最后，我们对此前一项研究的结论提出质疑——该研究曾报道该物种的绝大多数胞嘧啶甲基化均为不对称型。