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Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing

Suying Cao12, Jianyong Han1*, Jun Wu3, Qiuyan Li1, Shichao Liu4, Wei Zhang1, Yangli Pei1, Xiaoan Ruan5, Zhonghua Liu4, Xumin Wang6, Bing Lim5 and Ning Li1*

Author Affiliations

1 State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China

2 Animal Science and Technology College, Beijing University of Agriculture, Beijing, China

3 Novogene Bioinformatics Institute, Beijing, China

4 College of Life Science, Northeast Agricultural University, Haerbin, China

5 Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore, Singapore

6 Beijing Institute of Genomics, Chinese academy of Sciences, Beijing, China

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BMC Genomics 2014, 15:4  doi:10.1186/1471-2164-15-4

Published: 3 January 2014



Because few studies exist to describe the unique molecular network regulation behind pig pre-implantation embryonic development (PED), genetic engineering in the pig embryo is limited. Also, this lack of research has hindered derivation and application of porcine embryonic stem cells and porcine induced pluripotent stem cells (iPSCs).


We identified and analyzed the genome wide transcriptomes of pig in vivo-derived and somatic cell nuclear transferred (SCNT) as well as mouse in vivo-derived pre-implantation embryos at different stages using mRNA deep sequencing. Comparison of the pig embryonic transcriptomes with those of mouse and human pre-implantation embryos revealed unique gene expression patterns during pig PED. Pig zygotic genome activation was confirmed to occur at the 4-cell stage via genome-wide gene expression analysis. This activation was delayed to the 8-cell stage in SCNT embryos. Specific gene expression analysis of the putative inner cell mass (ICM) and the trophectoderm (TE) revealed that pig and mouse pre-implantation embryos share regulatory networks during the first lineage segregation and primitive endoderm differentiation, but not during ectoderm commitment. Also, fatty acid metabolism appears to be a unique characteristic of pig pre-implantation embryonic development. In addition, the global gene expression patterns in the pig SCNT embryos were different from those in in vivo-derived pig embryos.


Our results provide a resource for pluripotent stem cell engineering and for understanding pig development.