Transcriptional profiles of bovine in vivo pre-implantation development

BMC Genomics

Xiuchun (Cindy) Tian³  Jingbo Chen¹  Yijun Ruan⁵  Rachel O’Neill⁴  Jinbo Bi²  Yong Tang³  Craig Obergfell⁴  Xinbao Zheng¹  Oscar Luo⁵  Hong Dong¹  Jiangwen Sun²  Zongliang Jiang³ 

[1] Institute of Animal Science, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, P.R. China;Department of Computer Science and Engineering, School of Engineering, University of Connecticut, Storrs, Connecticut, USA;Center for Regenerative Biology, Department of Animal Science, University of Connecticut, Storrs, Connecticut, USA;Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA;The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA

关键词: Mouse;    Human;    Bovine;    Hub genes;    Stage specific module;    RNA-seq;    Embryonic genome activation;    Pre-implantation development;   

Others  :  1140922
DOI  :  10.1186/1471-2164-15-756

 received in 2014-05-15, accepted in 2014-08-29,  发布年份 2014

【 摘 要 】

Background

During mammalian pre-implantation embryonic development dramatic and orchestrated changes occur in gene transcription. The identification of the complete changes has not been possible until the development of the Next Generation Sequencing Technology.

Results

Here we report comprehensive transcriptome dynamics of single matured bovine oocytes and pre-implantation embryos developed in vivo. Surprisingly, more than half of the estimated 22,000 bovine genes, 11,488 to 12,729 involved in more than 100 pathways, is expressed in oocytes and early embryos. Despite the similarity in the total numbers of genes expressed across stages, the nature of the expressed genes is dramatically different. A total of 2,845 genes were differentially expressed among different stages, of which the largest change was observed between the 4- and 8-cell stages, demonstrating that the bovine embryonic genome is activated at this transition. Additionally, 774 genes were identified as only expressed/highly enriched in particular stages of development, suggesting their stage-specific roles in embryogenesis. Using weighted gene co-expression network analysis, we found 12 stage-specific modules of co-expressed genes that can be used to represent the corresponding stage of development. Furthermore, we identified conserved key members (or hub genes) of the bovine expressed gene networks. Their vast association with other embryonic genes suggests that they may have important regulatory roles in embryo development; yet, the majority of the hub genes are relatively unknown/under-studied in embryos. We also conducted the first comparison of embryonic expression profiles across three mammalian species, human, mouse and bovine, for which RNA-seq data are available. We found that the three species share more maternally deposited genes than embryonic genome activated genes. More importantly, there are more similarities in embryonic transcriptomes between bovine and humans than between humans and mice, demonstrating that bovine embryos are better models for human embryonic development.

Conclusions

This study provides a comprehensive examination of gene activities in bovine embryos and identified little-known potential master regulators of pre-implantation development.

【 授权许可】

   
2014 Jiang et al.; licensee BioMed Central Ltd.

【 图 表 】

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