Reproduction Abstracts

Measuring gene expression in individual cells is crucial for understanding the gene regulatory network controlling human embryonic development. Here we apply single-cell RNA sequencing (RNA-Seq) analysis to 124 individual cells from human preimplantation embryos and human embryonic stem cells (hESCs) at different passages. The number of maternally expressed genes detected in our data set is 22 687, including 8701 long noncoding RNAs (lncRNAs), which represents a significant increase from 9735 maternal genes detected previously by cDNA microarray. We discovered 2733 novel lncRNAs, many of which are expressed in specific developmental stages. To address the long-standing question whether gene expression signatures of human epiblast (EPI) and in vitro hESCs are the same, we found that EPI cells and primary hESC outgrowth have dramatically different transcriptomes, with 1498 genes showing differential expression between them. We also profiled DNA methylome dynamics during preimplantation development of human embryos. Our work provides insights of critical features of the transcriptome and DNA methylome landscapes of human early embryos, as well as the functional significance of DNA methylome to regulation of gene expression and repression of transposable elements.