Reconstituting the transcriptome and DNA methylome landscapes of human implantation

Fan Zhou, Rui Wang, Peng Yuan, Yixin Ren, Yunuo Mao, Rong Li, Ying Lian, Junsheng Li, Lu Wen, Liying Yan, Jie Qiao () and Fuchou Tang ()
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Fan Zhou: Peking University
Rui Wang: Peking University
Peng Yuan: Peking University
Yixin Ren: Peking University
Yunuo Mao: Peking University
Rong Li: Peking University
Ying Lian: Peking University
Junsheng Li: Peking University
Lu Wen: Peking University
Liying Yan: Peking University
Jie Qiao: Peking University
Fuchou Tang: Peking University

Nature, 2019, vol. 572, issue 7771, 660-664

Abstract: Abstract Implantation is a milestone event during mammalian embryogenesis. Implantation failure is a considerable cause of early pregnancy loss in humans1. Owing to the difficulty of obtaining human embryos early after implantation in vivo, it remains unclear how the gene regulatory network and epigenetic mechanisms control the implantation process. Here, by combining an in vitro culture system for the development human embryos after implantation and single-cell multi-omics sequencing technologies, more than 8,000 individual cells from 65 human peri-implantation embryos were systematically analysed. Unsupervised dimensionality reduction and clustering algorithms of the transcriptome data show stepwise implantation routes for the epiblast, primitive endoderm and trophectoderm lineages, suggesting robust preparation for the proper establishment of a mother-to-offspring connection during implantation. Female embryos showed initiation of random X chromosome inactivation based on analysis of parental allele-specific expression of X-chromosome-linked genes during implantation. Notably, using single-cell triple omics sequencing analysis, the re-methylation of the genome in cells from the primitive endoderm lineage was shown to be much slower than in cells of both epiblast and trophectoderm lineages during the implantation process, which indicates that there are distinct re-establishment features in the DNA methylome of the epiblast and primitive endoderm—even though both lineages are derived from the inner cell mass. Collectively, our work provides insights into the complex molecular mechanisms that regulate the implantation of human embryos, and helps to advance future efforts to understanding early embryonic development and reproductive medicine.

Date: 2019
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DOI: 10.1038/s41586-019-1500-0

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