Major differences in gene expression profiles revealed in day-25 trophoblast but not embryonic discs from cattle clones

To better understand the problems associated with cloning, gene expression profiling of AI- and SCNT-derived bovine (day 25 of pregnancy) fetuses was performed. The embryonic disc and the extraembryonic tissues for each fetus were analyzed separately using a bovine oligoarray. Clustering of all the expression profiles showed clustering by tissue, but no separation of AI vs. SCNT samples was observed. Statistical analysis using a mixed model revealed 188 differentially expressed genes between the extraembryonic tissues and 10 differentially expressed genes between the embryonic discs of AI- and SCNT-derived fetuses. Between the tissue types >9,000 genes showed differential expression, of which 2,127 that showed >=2-fold difference in expression. The data generated in the current experiment clearly shows that the main problem with SCNT pregnancies is related to abnormal gene expression in the extraembryonic tissues. Keywords: nuclear transfer Ref design with dye swap