Global gene expression profiles in male and female single bovine blastocysts. Bos taurus

X-chromosome reactivation (XCR) in early development was studied using transcriptome data from bovine male and female blastocysts derived by in vitro fertilization (IVF) or somatic cell nuclear transfer (SCNT). X-chromosome genes (X-genes) were upregulated almost twofold higher in female IVF blastocysts compared to that found in males. Since the mean expression levels of autosomal genes were relatively constant in both males and females, the upregulation of X-genes in female IVFs demonstrated a transcriptional sexual dimorphism between the sexes. X-genes were similarly expressed in inner cell mass and trophectoderm cells of female blastocysts, indicating no imprinted inactivation of paternal X in trophectoderm. Whereas the distribution of female-to-male expression ratios for autosomal genes was well balanced in IVFs, the distribution of X-genes was biased towards females such that approximately 80% of X- genes showed an increased level of expression. These observations of XCR and of X and autosomal gene expressions in IVFs were found in SCNTs, although to a lesser extent than that found in IVFs. We found that sham SCNT blastocysts, which underwent the same nuclear transfer procedures but retained their embryonic genome, closely mimicked that found with IVFs, and therefore, demonstrated that embryo manipulation itself did not interrupt XCR. In addition, from a heatmap of X-gene expression, we found a distinctive pattern between the sexes in which female SCNTs differed from male SCNTs and donor cells, but resembled female IVFs. Our findings that female IVFs, and to a lesser extent female SCNTs, undergo XCR, demonstrate that clonal reprogramming of bovine X chromosomes is incomplete and varies not only among local chromosomal regions but also among individual blastocysts. Overall design: Males or females blastocysts generated by in-vitro fertilization (IVF), somatic cell nuclear transfer (SCNT), or sham-SCNT manipulation along with the donor cells used in the SCNT process.