Date of Completion


Embargo Period



pre-implantation development, RNA-seq, Microarray, Imprinting, Brm, Baf170, Induced pluripotent stem cells, Reprogramming, bovine, Pig, human, mouse

Major Advisor

Dr. Xiuchun (Cindy) Tian

Associate Advisor

Dr. Rachel O'neill

Associate Advisor

Dr. Robert Milvae

Associate Advisor

Dr. Young Tang

Field of Study

Animal Science


Doctor of Philosophy

Open Access

Open Access


Understanding of transcriptional machinery of early embryo development and epigenetic mechanisms of reprogramming is essential for embryogenesis and the success of animal biotechnology. This dissertation presents (1) transcriptional profiles of bovine in vivo pre-implantation development (Chapter Two); (2) bovine imprinted gene expression patterns across mammalian species (Chapter Three); (3) effects of High Hydrostatic Pressure (HHP) on expression profiles of in vitro produced embryos (Chapter Four); (4) roles of BAF complex in reprogramming (Chapter Five).

In the first section, we reported comprehensive transcriptome dynamics of single matured bovine oocytes and pre-implantation embryos developed in vivo using the RNA-seq technologies. Subsequently, using weighted gene co-expression network analysis, we found 12 stage-specific modules of co-expressed genes and identified potential master regulators of embryo development. Finally, we conducted the first comparison of embryonic expression profiles across three mammalian species, human, mouse and bovine. We found that the three species share more maternally deposited genes than embryonic genome activated genes and demonstrated that bovine embryos are better models for human embryonic development.

With the “gold standards” in vivo embryo transcriptome datasets, we characterized all currently known bovine imprinted genes and compared them to their counterparts in humans, mice and pigs in the second section. We found interesting expression patterns such as high levels of paternally expressed and low levels of maternally expressed genes in bovine oocytes. We also report drastic variations of species-specific levels of expression of imprinted genes.

In the third section, we evaluated the effects of HHP on the transcriptome of bovine IVF blastocysts by the DNA Microarray technology. We found a positive effect of HHP on bovine IVF blastocysts mediated by specific gene expression changes.

In the fourth section, we aimed to better understand the mechanism of reprogramming and to further improve its efficiency by studying the roles of somatic BAF components, Brm and Baf170, during reprogramming in the mouse model. We found that Brm and Baf170 inhibit reprogramming in a stage-specific fashion. We further showed that inhibiting somatic BAF improves complete reprogramming by facilitating the activation of the “pluripotency circuitry” and by constituting to the Stat3-regulated epigenetic network during pluripotency establishment.