Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome.
Detecting rare asymmetrically methylated cytosines and decoding methylation patterns in the honeybee genome.
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DOI：
10.1098/rsos.170248
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发表时间：
2017-09
影响因子：
3.5
通讯作者：
Foret S
中科院分区：
文献类型：
--
作者：
Welsh L;Maleszka R;Foret S
真核生物中依赖于上下文的基因表达受到多种机制的控制，包括主要发生在CG二核苷酸（CpGs）中的胞嘧啶甲基化。然而，不太频繁的非CpG不对称甲基化已被发现在各种细胞类型，如哺乳动物神经元，最近的结果表明，这些网站可以抑制转录独立的CpG上下文。此外，一个新兴的观点是，CpG半甲基化可能不仅来自细胞过程的失调，而且也是甲基化组的标准特征。在这里，我们已经应用了一种新的方法来检查是否不对称的CpG甲基化存在于一个稀疏甲基化的基因组的蜜蜂，社会昆虫具有高水平的表观遗传驱动的表型可塑性。通过将illustrator基因的链特异性超深度扩增子测序与全基因组甲基化组学和生物信息学相结合，我们表明可以在蜜蜂基因组中明确检测到罕见的不对称甲基化CpG。此外，我们确认两个表型和生殖不同的种姓，皇后和工人之间的差异甲基化，并提供新的洞察大脑甲基化模式的异质性。特别是，我们挑战的假设，对称的甲基化水平反映了对称的甲基化模式，并得出结论，半甲基化可能发生的频率比甲基化水平。最后，我们质疑以前的研究，其中大部分的胞嘧啶甲基化在这个物种被报道为不对称的有效性。
Context-dependent gene expression in eukaryotes is controlled by several mechanisms including cytosine methylation that primarily occurs in the CG 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 CpG hemimethylation 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 whether asymmetric CpG methylation is present in a sparsely methylated genome of the honeybee, 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 CpGs can be unambiguously detected in the honeybee 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.
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影响因子：
25
作者：
Guo, Junjie U.;Su, Yijing;Shin, Joo Heon;Shin, Jaehoon;Li, Hongda;Xie, Bin;Zhong, Chun;Hu, Shaohui;Le, Thuc;Fan, Guoping;Zhu, Heng;Chang, Qiang;Gao, Yuan;Ming, Guo-li;Song, Hongjun
通讯作者：
Song, Hongjun
蜜蜂转录组的表观遗传调控：揭示甲基化基因的本质。
影响因子：
4.4
作者：
Foret S;Kucharski R;Pittelkow Y;Lockett GA;Maleszka R
通讯作者：
Maleszka R
影响因子：
3.9
作者：
Gagne A;Hochman A;Qureshi M;Tong C;Arbon J;McDaniel K;Davis TL
通讯作者：
Davis TL
影响因子：
4.4
作者：
Remnant EJ;Ashe A;Young PE;Buchmann G;Beekman M;Allsopp MH;Suter CM;Drewell RA;Oldroyd BP
通讯作者：
Oldroyd BP
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y