Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology, School of Life Sciences, Third Hospital, Peking University, Beijing, China.
Biomedical Pioneering Innovaiton Center, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing, China.
PLoS Biol. 2020 Jul 30;18(7):e3000799. doi: 10.1371/journal.pbio.3000799. eCollection 2020 Jul.
Epigenetic dynamics, such as DNA methylation and chromatin accessibility, have been extensively explored in human preimplantation embryos. However, the active demethylation process during this crucial period remains largely unexplored. In this study, we use single-cell chemical-labeling-enabled C-to-T conversion sequencing (CLEVER-seq) to quantify the DNA 5-formylcytosine (5fC) levels of human preimplantation embryos. We find that 5-formylcytosine phosphate guanine (5fCpG) exhibits genomic element-specific distribution features and is enriched in L1 and endogenous retrovirus-K (ERVK), the subfamilies of repeat elements long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs), respectively. Unlike in mice, paired pronuclei in the same zygote present variable difference of 5fCpG levels, although the male pronuclei experience stronger global demethylation. The nucleosome-occupied regions show a higher 5fCpG level compared with nucleosome-depleted ones, suggesting the role of 5fC in organizing nucleosome position. Collectively, our work offers a valuable resource for ten-eleven translocation protein family (TET)-dependent active demethylation-related study during human early embryonic development.
表观遗传动力学，如 DNA 甲基化和染色质可及性，在人类胚胎着床前已被广泛研究。然而，在此关键时期的主动去甲基化过程仍在很大程度上未被探索。在这项研究中，我们使用单细胞化学标记辅助的 C 到 T 转换测序 (CLEVER-seq) 来定量人类胚胎着床前胚胎的 5- 甲酰胞嘧啶 (5fC) 水平。我们发现 5- 甲酰胞嘧啶磷酸鸟嘌呤 (5fCpG) 表现出基因组元件特异性的分布特征，分别在长散布核元件 (LINEs) 的 L1 和内源性逆转录病毒-K (ERVK) 以及长末端重复 (LTR) 的亚家族中富集。与在小鼠中不同，同一受精卵中的配对原核呈现出不同的 5fCpG 水平差异，尽管雄性原核经历更强的全局去甲基化。核小体占据区域的 5fCpG 水平高于核小体缺失区域，表明 5fC 在组织核小体位置方面的作用。总的来说，我们的工作为在人类早期胚胎发育过程中，TET 依赖性的活性去甲基化相关研究提供了有价值的资源。
