ARS | Publication request: SERIAL ANALYSIS OF GENE EXPRESSION (SAGE) DURING ELONGATION OF PERI-IMPLANTATION PORCINE TROPHECTODERM (CONCEPTUS)

Submitted to: Physiological Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 5, 2004
Publication Date: November 9, 2004
Citation: Blomberg, L., Long, E.L., Sonstegard, T.S., Van Tassell, C.P., Dobrinsky, J.R., Zuelke, K.A. 2004. Serial analysis of gene expression (sage) during elongation of peri-implantation porcine trophectoderm (conceptus). Physiological Genomics. 20:188-194.

Interpretive Summary: The application of SAGE allowed the identification of over 430 transcripts displaying differential expression during D11 to D12 pig embryo development. Greater than half of these SAGE tags matched a sequence in the TIGR or NCBI databases and many of those assigned a gene annotation represented potential functions that could be important for efficient embryo development. To provide a more detailed and complete profile of gene expression during pig embryo development, we are currently analyzing the constitutively expressed tags, the major fraction of annotated tags. Furthermore, progress in the elucidation of the pig genome should enable future identification of currently unmatched SAGE tags thus providing additional information regarding the embryonic transcriptome at these stages. As illustrated by the example of the steroidogenic pathway, the capability of SAGE to achieve simultaneous expression measurements of numerous genes will enable the assemblage of genes, based on their function and metabolic pathway relationships, and could thereby provide the basis for establishing comprehensive physiologic models of embryo development.

Technical Abstract: Swine reproduction is plagued by significant embryo loss during the pre-implantation and early post-implantation period. The majority of embryonic loss typically occurs between gestational day (D) 11 and D12 during elongation of the trophoectoderm. Transcript profiles of D11 and D12 embryos should help elucidate the temporally regulated genes essential for tracking development efficacy. Serial analysis of gene expression (SAGE) libraries were constructed to establish qualitative and quantitative gene expression profiles from in vivo derived D11 and D12 swine embryos. A total of 42,389 tags (D11) and 42,391 tags (D12) representing 14,464 and 13,098 putative unique transcripts, respectively, were generated and statistical analysis of SAGE tag frequencies indicated that 431 tags were differentially expressed between libraries (p<0.05). Comparative sequence alignments of SAGE tags to Genbank nt and the Institute for Genomic Research (TIGR) porcine gene index databases provided tag annotation and subsequent assignment of gene ontology. Real-time PCR confirmed the differential expression between D11 and D12 of cytochrome p450scc (CYP11A1), aromatase (CYP19A), steroidogenic acute regulatory protein (STAR), microsomal glutathione S-transferase 1 (MGST1), and copper-zinc superoxide dismutase (SOD1), which belong to gene expression pathways critical for steroidogenesis and the oxidative stress response. Despite limited availability of species-specific transcript sequence data, porcine SAGE tags proved effective in identifying genes potentially crucial to embryo elongation and should enable the elucidation of a more comprehensive picture of the porcine transcriptome during embryo development.