Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation.
Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation.
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DOI：
10.1186/s12864-016-2506-8
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发表时间：
2016-03-12
期刊：
影响因子：
4.4
通讯作者：
Oldroyd BP
中科院分区：
文献类型：
--
作者：
Remnant EJ;Ashe A;Young PE;Buchmann G;Beekman M;Allsopp MH;Suter CM;Drewell RA;Oldroyd BP
性间基因组冲突有时会导致后代中父源和母源等位基因的不平等表达，从而产生亲本效应。在蜜蜂中，相互杂交可以显示出强烈的起源父母效应，支持基因组印记发生在这个物种中的理论预测。蜜蜂中印记背后的机制尚不清楚，但卵子和精子中的差异DNA甲基化表明可能涉及DNA甲基化。尽管如此，由于DNA甲基化是多功能的，很难将印迹与甲基化的其他作用分开。在这里，我们使用一种新的方法来研究蜜蜂中的亲本DNA甲基化。在意大利蜜蜂（Apis mellifera capensis）的亚种中，雌性的生殖可以通过精子与卵子受精进行，也可以通过孤雌生殖，产生来自两个母体基因组的雌性胚胎。我们比较了由女王产下的有性生殖二倍体胚胎与由她的女儿产下的孤雌生殖二倍体胚胎的全基因组甲基化模式。与受精胚胎相比，继承两个母体基因组的Thelytokous胚胎具有更少的高甲基化基因，这支持了受精胚胎由于继承了父亲基因组而增加甲基化的预测。然而，亚硫酸氢盐PCR和测序的差异甲基化基因，斯坦（GB 18207）显示出强烈的等位基因特异性甲基化，保持在受精和thelytokous胚胎。对于该基因，甲基化与单倍型相关，而不是与起源的亲本相关。我们的研究结果与基因组印记亲属理论的预测是一致的。然而，我们基于序列的等位基因特异性甲基化的证明表明，全基因组差异甲基化研究可能会混淆印迹和等位基因特异性甲基化。它进一步表明甲基化模式是可遗传的，或者特定的序列基序是某些基因中甲基化的目标。本文的在线版本（doi：10.1186/s12864-016-2506-8）包含补充材料，可供授权用户使用。
Intersexual genomic conflict sometimes leads to unequal expression of paternal and maternal alleles in offspring, resulting in parent-of-origin effects. In honey bees reciprocal crosses can show strong parent-of-origin effects, supporting theoretical predictions that genomic imprinting occurs in this species. Mechanisms behind imprinting in honey bees are unclear but differential DNA methylation in eggs and sperm suggests that DNA methylation could be involved. Nonetheless, because DNA methylation is multifunctional, it is difficult to separate imprinting from other roles of methylation. Here we use a novel approach to investigate parent-of-origin DNA methylation in honey bees. In the subspecies Apis mellifera capensis, reproduction of females occurs either sexually by fertilization of eggs with sperm, or via thelytokous parthenogenesis, producing female embryos derived from two maternal genomes. We compared genome-wide methylation patterns of sexually-produced, diploid embryos laid by a queen, with parthenogenetically-produced diploid embryos laid by her daughters. Thelytokous embryos inheriting two maternal genomes had fewer hypermethylated genes compared to fertilized embryos, supporting the prediction that fertilized embryos have increased methylation due to inheritance of a paternal genome. However, bisulfite PCR and sequencing of a differentially methylated gene, Stan (GB18207) showed strong allele-specific methylation that was maintained in both fertilized and thelytokous embryos. For this gene, methylation was associated with haplotype, not parent of origin. The results of our study are consistent with predictions from the kin theory of genomic imprinting. However, our demonstration of allele-specific methylation based on sequence shows that genome-wide differential methylation studies can potentially confound imprinting and allele-specific methylation. It further suggests that methylation patterns are heritable or that specific sequence motifs are targets for methylation in some genes. The online version of this article (doi:10.1186/s12864-016-2506-8) contains supplementary material, which is available to authorized users.