Document Type

Thesis - Open Access

Award Date


Degree Name

Master of Science (MS)


Mathematics and Statistics

First Advisor

Xijin Ge


Obox, preimplantation embryo development, single cell RNA sequencing


Preimplantation embryo development (PED) refers to the period from fertilization to implantation in mammals. This complex process is critical for successful implantation and pregnancy. Although studies on PED have been conducted, using mainly the mouse as a model organism, the gene regulatory mechanisms are still not well understood. The next-generation sequencing technologies enable researchers to obtain the genome-wide expression profiling with single-cell resolution, which are powerful tools to study early embryogenesis. We used the single-cell RNA sequencing datasets that are available in the public domain and conducted bioinformatics analysis of expression profiling from zygote to blastocyst. Through hierarchical clustering of the global expression profile, which appeared dynamically during PED, we identified Obox gene family and encoded the homeodomain-containing transcription factors. Accumulating evidence suggests that homeodomain genes play essential roles in early embryonic development. To investigate whether Obox family has similar roles, we comprehensively analyzed their sequences, showing that Obox are conserved genes that share from 58.78% to 98.85% of DNA identity. Subsequently, we investigated the homeodomain entropies and 3D-structures. The results indicated that Obox homeodomains show polymorphism and have a typical architecture of transcription factor. Additionally, the microarray investigation and orthologous protein analysis revealed that Obox are mouse-specific genes, expressed specifically in embryo cells. Furthermore, the phylogenetic structure of Obox indicated that Obox5 and Obox6 are located on different clades; Obox1 and Obox2 have the closest relation and share the common ancestor with Obox3. In addition, the evolution of Obox gave a rise to a mass of pseudogenes (47 were found in Emsembl), which implied that retrotransposons could affect the activation of Obox genes. We analyzed Obox genomic sequences by scanning the LTR retrotransposons showing that 5’-UTR of Obox contain LTR elements and belong to ERV-1, ERVL-MaLR and ERVK family. Due to the binding motif of Obox3 has been experimentally identified. Our hypothesis, which proposed that Obox3 functions as a transcription factor to regulate the genes that have similar expression pattern, has been tested by simulating binding on promoter regions. Overall, 12.35% (42/340) of genes’ promoter regions (p < 0.001) can be potentially bound by Obox3. These 340 genes share the same expression pattern with Obox3. All of these discoveries suggest that the Obox proteins may play a unique role in regulating gene expression during preimplantation embryo development. It has important implications for future studies on the identification of Obox signal pathway to explore the mechanism of PED.

Library of Congress Subject Headings

Mice -- Embryos.
Gene expression.


Includes bibliographical references (pages 73-76)



Number of Pages



South Dakota State University


Copyright © 2016 Wei Wang