Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP proteins in Coprinopsis cinerea [RNA-seq]. Coprinopsis cinerea

TET/JBP enzymes oxidize 5-methylpyrimidines in DNA. In mammals, the oxidized methylcytosines (oxi-mC) function as epigenetic marks and likely intermediates in DNA demethylation. Here we present a novel diglucosylation-based method to simultaneously map 5hmC, 5fC and 5caC at near base-pair resolution, and verify the results using independent methods. We have used the method to map the distribution of oxi-mC across the genome of Coprinopsis cinerea, a basidiomycete that encodes 47 TET/JBP paralogs in a new class of DNA transposons. Like 5-methylcytosine (5mC) residues from which they are derived, oxi-mC modifications are enriched at centromeres, TET/JBP transposons, and multicopy paralogous genes that are not expressed, but rarely mark genes whose expression changes between two developmental stages. Our study provides evidence for the emergence of an epigenetic regulatory system through recruitment of selfish elements in a eukaryotic lineage, and describes a method to map all three different species of oxi-mC simultaneously. Overall design: RNA-seq in Oidia and Hyphae (Coprinopsis cinerea).

TET/JBP酶（TET/JBP enzymes）可氧化DNA中的5-甲基嘧啶。在哺乳动物体内，氧化型甲基胞嘧啶（oxi-mC）作为表观遗传标记，同时可能是DNA去甲基化过程的中间产物。本文报道一种基于双糖基化的全新实验方法，可在接近碱基对的分辨率下同时定位5-羟甲基胞嘧啶（5hmC）、5-甲酰基胞嘧啶（5fC）与5-羧基胞嘧啶（5caC），并通过独立实验方法验证了该方法的有效性。研究团队利用该方法对灰盖鬼伞（Coprinopsis cinerea）的全基因组氧化型甲基胞嘧啶分布进行了图谱绘制，该担子菌在一类新型DNA转座子（DNA transposons）中编码47个TET/JBP旁系同源基因。与其衍生自的5-甲基胞嘧啶（5mC）残基类似，氧化型甲基胞嘧啶修饰富集于着丝粒、TET/JBP转座子以及未表达的多拷贝旁系同源基因区域，却极少标记在两个发育阶段间表达存在差异的基因。本研究证实了真核生物谱系中通过招募自私遗传元件而催生表观遗传调控系统的现象，并报道了一种可同时定位三类氧化型甲基胞嘧啶的实验方法。整体实验设计：对灰盖鬼伞的粉孢子与菌丝体开展转录组测序（RNA-seq）。