title: Specific gene-regulation networks during the pre-implantation development of the pig embryo as revealed by deep sequencing.
abstract: BACKGROUND
  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).
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  Our results provide a resource for pluripotent stem cell engineering and for understanding pig development.
authors.forename: Suying
authors.initials: S
authors.lastname: Cao
authors.affiliation: State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China. hanjy@cau.edu.cn.
authors.forename: Jianyong
authors.initials: J
authors.lastname: Han
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
authors.forename: Qiuyan
authors.initials: Q
authors.lastname: Li
authors.forename: Shichao
authors.initials: S
authors.lastname: Liu
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.forename: Yangli
authors.initials: Y
authors.lastname: Pei
authors.forename: Xiaoan
authors.initials: X
authors.lastname: Ruan
authors.forename: Zhonghua
authors.initials: Z
authors.lastname: Liu
authors.forename: Xumin
authors.initials: X
authors.lastname: Wang
authors.forename: Bing
authors.initials: B
authors.lastname: Lim
authors.forename: Ning
authors.initials: N
authors.lastname: Li
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D001755:Blastocyst / Q000378:metabolism*; D004475:Ectoderm / Q000378:metabolism; D004622:Embryo, Mammalian / Q000166:cytology / Q000378:metabolism*; D047108:Embryonic Development; D005227:Fatty Acids / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D005818:Genetic Engineering; D008040:Genetic Linkage; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D008810:Mice, Inbred C57BL; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013552:Swine; D059467:Transcriptome
chemical_list: D015415:Biomarkers; D005227:Fatty Acids; D012333:RNA, Messenger