Doctor of Philosophy (PhD)


Department of Animal Sciences

Document Type



Early embryo loss has been identified as one of the main problems affecting fertility of both agricultural important animals and humans. However, most of the molecular and cellular mechanisms that lead to establishment of pregnancy and formation of a functional placenta during pre- and peri-implantation developmental period in human and cattle remain unknown. This dissertation presents mechanisms regulating bovine early embryonic development the molecular dynamics of human placental trophoblast lineage differentiation and development.

First, by using improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), we characterized the landscape of chromatin dynamics of bovine oocytes and early embryos. We found that chromatin accessibility is low in oocytes and 2-/4-cell embryos, followed by a significant increase during major embryonic genome activation (EGA). We also identified the critical chromatin signatures that differ between in vivo and in vitro derived blastocysts, which shares insights to the potential mechanisms leading to low quality of embryos produced in vitro. Motivated by this, we next performed single-cell RNA sequencing of bovine blastocyst embryos derived from in vivo (IVV) and in vitro fertilization (IVC), and in vitro cultured in reduced nutrients (IVR). We found IVV embryos have well defined epiblasts with better developmental potential compared to the IVC counterpart. We also elucidated how the reduced nutrient culture condition regulates the cell functions and pathways to benefit bovine embryo competence.

Then we performed single-cell RNA sequencing of cells from cultured human blastocysts and defined the transcriptomic landscape of placental trophoblast (TB) that surrounds the epiblast and associated embryonic tissues during the enigmatic day 8 to day 12 peri-implantation period. We found, over the 5 day of culture, two trophoblast sublineages emerged from a progenitor stem cell population. One was syncytial and produced placental hormones. The second became motile and expressed genes associated with the innate immune system and invasion. Followed by that, we performed comprehensive transcriptomic characterizations of trophoblast lineage differentiation and development using three widely used in vitro trophoblast models. We revealed the identities of trophoblast lineages from three models that mimic human early trophoblast development, and identified and validated novel trophoblast lineage markers.



Committee Chair

Jiang, Zongliang (Carl)



Available for download on Friday, February 22, 2030