5-Formylcytosine Landscapes of Human Preimplantation Embryos at Single-cell Resolution

The epigenetic regulation containing DNA methylation and chromatin accessibility have been extensively explored in human preimplantation development. However, the dynamic of demethylation in this crucial process remains largely unknown. In this study, we use CLEVER-seq to quantify the DNA 5-formylcytosine (5fC) level of human early embryos. The distribution of 5fC exhibits genomic region preference and are enriched in L1 and ERVK, subfamily of repeat element. Unlike in mice, the paired pronuclei presents inconsistent 5fC level although the male pronuclei experiences stronger demethylation. And the centre of 5fC shows less accessible genome especially in proximal region. Collectively, our work offers new insight into the understanding of the complex demethylation in early human embryo development. In total, we sequenced 130 euploid single cell without copy number viriation (CNV) . The sampling stages covered sperm, oocyte, the first polarbody, tow-cell, four-cell, eight-cell, morula, inner cell mess, trophoectoderm and hESC. The synthesized model DNA contain 5fC modification was spiked in each sample to quantify the efficiency of malononitrile labelling. The average conversion rate was 79.6% in total 130 samples. With ~5× sequencing depth of each single-cell sample, the average clean reads of each sample is 116.8 million with 74.6% averaged mapping rate. 24,830 to 45,398 5fCpG sites were identified from merged same stage samples. The raw data have been deposited in GSA for Human (https://bigd.big.ac.cn/gsa-human/) under accession HRA000194 due to privacy concerns.