Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland.
Biological Sciences, Monash University, Clayton, VIC, Australia.
Genome Biol. 2018 Jan 25;19(1):9. doi: 10.1186/s13059-017-1383-z.
In plants, the existence and possible role of epigenetic reprogramming has been questioned because of the occurrence of stably inherited epialleles. Evidence suggests that epigenetic reprogramming does occur during land plant reproduction, but there is little consensus on the generality and extent of epigenetic reprogramming in plants. We studied DNA methylation dynamics during the life cycle of the liverwort Marchantia polymorpha. We isolated thalli and meristems from male and female gametophytes, archegonia, antherozoids, as well as sporophytes at early and late developmental stages, and compared their DNA methylation profiles.
Of all cytosines tested for differential DNA methylation, 42% vary significantly in their methylation pattern throughout the life cycle. However, the differences are limited to few comparisons between specific stages of the life cycle and suggest four major epigenetic states specific to sporophytes, vegetative gametophytes, antherozoids, and archegonia. Further analyses indicated clear differences in the mechanisms underlying reprogramming in the gametophytic and sporophytic generations, which are paralleled by differences in the expression of genes involved in DNA methylation. Differentially methylated cytosines with a gain in methylation in antherozoids and archegonia are enriched in the CG and CHG contexts, as well as in gene bodies and gene flanking regions. In contrast, gain of DNA methylation during sporophyte development is mostly limited to the CHH context, LTR retrotransposons, DNA transposons, and repeats.
We conclude that epigenetic reprogramming occurs at least twice during the life cycle of M. polymorpha and that the underlying mechanisms are likely different between the two events.
在植物中，由于稳定遗传的表观等位基因的存在，人们质疑是否存在表观遗传重编程。有证据表明，表观遗传重编程确实发生在陆地植物繁殖过程中，但对于植物中表观遗传重编程的普遍性和程度尚未达成共识。我们研究了苔类植物 Marchantia polymorpha 生命周期中的 DNA 甲基化动态。我们从雌雄配子体、颈卵器、精子囊中分离出叶状体和分生组织，以及处于早期和晚期发育阶段的孢子体，并比较了它们的 DNA 甲基化谱。
在所测试的所有用于差异 DNA 甲基化的胞嘧啶中，有 42% 在整个生命周期中其甲基化模式发生显著变化。然而，这些差异仅限于生命周期特定阶段之间的少数比较，并表明了与孢子体、营养配子体、精子和颈卵器特定的四个主要表观遗传状态。进一步的分析表明，在配子体和孢子体世代中，重编程的机制存在明显差异，这与参与 DNA 甲基化的基因表达差异相平行。在精子和颈卵器中，获得甲基化的差异甲基化胞嘧啶在 CG 和 CHG 环境中以及在基因体和基因侧翼区域中富集。相比之下，在孢子体发育过程中获得 DNA 甲基化主要限于 CHH 环境、LTR 反转录转座子、DNA 转座子和重复序列。
我们得出结论，表观遗传重编程至少在 M. polymorpha 的生命周期中发生两次，并且两个事件的潜在机制可能不同。
