Characterization and comparative analyses of transcriptomes for in vivo and in vitro produced peri-implantation conceptuses and endometria from sheep.

Epidemiological studies indicate that in vitro–produced (IVP) embryos can predispose offspring to a series of health problems, including preterm birth, perinatal mortality [1], low birth weight [1, 2], and congenital malformations [3], as well as long‑term risk of disease [4]. Another problem with in vitro fertilization (IVF)-assisted reproduction techniques is embryo implantation failure. Although embryonic and endometrial factors can contribute to embryonic implant failure, it is more likely caused by endometrial factors in females with good-quality embryos. The endometrium serves as an early sensor of embryos, and the pattern of endometrial gene expression when the embryo becomes attached to the mother’s uterus could account for the final outcome of a pregnancy [5]. Unfortunately, IVP has been reported to induce disorders in the endometrium [6,7,8]. Therefore, understanding IVP-induced changes in both the conceptus and the endometrium during the peri-implantation period is critical for preventing embryonic implant failure and other IVP-induced side effects. While global gene expression patterns (transcriptomes) of IVP embryos have been analyzed in many species, including mice [9,10], cows [11,12,13,14], pigs [15,16], and sheep [17,18,19,20,21], using various high‑throughput methods (microarrays and RNA sequencing [22, 23]), the factors affecting embryonic implantation remain elusive. Moreover, deep sequencing has not yet been applied to analyze the effects of IVP on gene expression in the conceptus and endometrium during the peri-implantation period. Therefore, in this study, we explored IVP-induced changes in the conceptus and endometrium using a digital gene expression (DGE) method to acquire transcriptome data for sheep. In addition, as previous research has shown that there are differences in the structure and biological functions associated with the caruncular (C) and intercaruncular (IC) areas of the endometrium [24], we separately analyzed two distinct endometrial zones. We chose to analyze gene expression on day 17, which is the critical implantation window for pregnancy, as this is when intimate adhesion between the trophoblast and the uterine luminal epithelium begins in sheep. The aim of this comparative analysis of transcriptome profiles of the IVO and IVP groups was to provide a reference transcriptome for understanding the molecular origins and underlying mechanism (s) that lead to aberrations in the conceptus–endometrial interactions and subsequently, to IVP induced disorders. Therefore, in the present study, we investigated the differences in gene expression profiles between control in vivo produced (IVO, i.e., in vivo fertilized followed by further development in the uterus) and in vitro produced (IVP, i.e., IVF followed by further culture in the incubator) conceptuses and the endometria in sheep.