26Multipotent trophoblasts undergo dynamic morphological movement and cellular 27 differentiation after embryonic implantation to generate placenta. However, the 28 mechanism controlling trophoblast development and differentiation during 29 peri-implantation development remains elusive. In this study, we modeled human 30 embryo peri-implantation development from blastocyst to early post-implantation 31 stages by using an in vitro coculture system, and profiled the transcriptome of 32 individual trophoblast cells from these embryos. We revealed the genetic networks 33 regulating peri-implantation trophoblast development. While determining when 34 trophoblast differentiation happens, our bioinformatic analysis identified T-box 35 transcription factor 3 (TBX3) as a key regulator for the differentiation of 36 cytotrophoblast into syncytiotrophoblast. The function of TBX3 in trophoblast 37 differentiation is then validated by a loss-of-function experiment. In conclusion, our 38 results provided a valuable resource to study the regulation of trophoblasts 39 development and differentiation during human peri-implantation development. 40 41 Keywords: Single-cell RNA sequencing, Peri-implantation embryo development, 42 Trophoblasts differentiation, TBX3 43 44 Background 45 The placenta is the interface between the fetal and maternal circulation, and plays 46 an essential role in supporting fetus development and survival. Most placental 47 functions are carried out by trophoblasts, which are derived from the trophectoderm 48 (TE) in blastocysts [1]. After implantation, the trophectoderm becomes multipotent 49 trophoblast stem cells, proliferate and differentiate into distinct trophoblast 50 sublineages, including cytotrophoblast (CT), extravillous cytotrophoblast (EVT) and 51 syncytiotrophoblast (ST) [2].52 53 Previous anatomical studies using a relatively small number of human specimens 54 have shown that the CT appears right after implantation, which then differentiates into 55 the EVT and ST before day 21 post-fertilization [3]. Recent studies using single cell 56 RNA-seq on human placenta successfully revealed transcriptomic and functional 57 heterogeneity between different trophoblast sublineages within placenta. However, all 58 these single cell profiling studies used placenta after 6 gestational weeks [4-7]. Due to 59 the lacking of data for early-post implantation embryos, it is still elusive when 60 trophoblast sublineages are established, and how the trophoblast differentiation is 61 regulated. 62 63 Human embryos cocultured with endometrial cells in vitro can model 64 morphological and molecular changes of peri-implantation embryos in vivo [8-10]. In 65 this study, we profiled transcriptomes of 476 individual trophoblast cells isolated from 66 19 human embryos co-cultured with endometrial cells. . We revealed the regulatory 67 networks underlying trophoblast development and differentiation. Using a unique 68 bioinformatic approach and a loss-of-function verification experiments, we identified 69 a novel transc...