Identification of N6-adenine methylation in C. elegans DNA

In mammalian cells, DNA methylation on the 5th position of cytosine (5mC) plays an important role as an epigenetic mark. However, DNA methylation was considered to be absent in C. elegans because of the lack of detectable 5mC as well as homologs of the cytosine DNA methyltransferases. Here, using multiple approaches, we demonstrate the presence of adenine N6-methylation (6mA) in C. elegans DNA. We further demonstrate that this modification increases trans-generationally in a paradigm of epigenetic inheritance. Importantly, we identify a DNA demethylase, NMAD-1, and a potential DNA methyltransferase, DAMT-1, which regulate 6mA levels and crosstalk between methylation of histone H3K4me2 and 6mA, and control the epigenetic inheritance of phenotypes associated with the loss of the H3K4me2 demethylase spr-5. Together, these data identify a novel DNA modification in C. elegans and raise the exciting possibility that 6mA may be a carrier of heritable epigenetic information in eukaryotes. Overall design: SMRT-sequencing for a mixed cell population of wildtype worms 6mA ChIP-Seq for a mixed cell population of wildtype worms

在哺乳动物细胞中，胞嘧啶第5位的DNA甲基化（5mC）作为表观遗传标记发挥关键功能。然而，由于未检测到5mC且未发现胞嘧啶DNA甲基转移酶的同源蛋白，秀丽隐杆线虫（C. elegans）曾被认为不存在DNA甲基化修饰。本研究通过多种实验手段，证实秀丽隐杆线虫（C. elegans）的DNA中存在腺嘌呤N6-甲基化修饰（6mA）。我们进一步发现，该修饰在表观遗传遗传模型中呈现跨代积累的现象。尤为重要的是，本研究鉴定出一种DNA去甲基化酶NMAD-1与一种潜在的DNA甲基转移酶DAMT-1，二者可调控6mA的水平，介导组蛋白H3K4me2甲基化与6mA修饰之间的交叉互作，并调控与H3K4me2去甲基化酶spr-5缺失相关表型的表观遗传传递。综上，本研究在秀丽隐杆线虫中发现了一种全新的DNA修饰，并提出了一个引人关注的科学假说：6mA可能是真核生物中可遗传表观遗传信息的载体。实验整体设计：1. 野生型线虫混合细胞群体的单分子实时测序（SMRT测序）；2. 野生型线虫混合细胞群体的6mA染色质免疫沉淀测序（6mA ChIP-Seq）