Dissection of embryo- and progesterone-induced transcriptome changes in bovine endometrium during the pre-attachment stage

Abstract

The preparation of the endometrium for the process of embryo implantation is critical for the establishment of a pregnancy. There are two major effects on the bovine endometrium during the pre-implantation period important for successful implantation – embryo-derived signals (e.g. interferon tau) and ovarian progesterone. To distinguish between these two effects a biological model was analyzed comprised of three different groups: day 18 pregnant animals after artificial insemination (AI), day 18 controls with high serum progesterone levels (CPH) and day 18 controls with low serum progesterone levels (CPL). RNA was isolated from endometrial samples of the ipsilateral caudal uterine horns and analyzed with the Affymetrix Bovine Genome Array and a custom-made Bovine oviduct epithelium and endometrium (BOE) cDNA array. The BOE array consists of approximately 1000 mRNAs, which were identified as regulated in bovine endometrium or oviduct epithelium during the estrous cycle or during early pregnancy in previous studies. The normalized data (BioConductor packages plier for Affymetrix and vsn for BOE array) were analyzed with SAM (Significance Analysis of Microarrays) to detect significant changes of mRNA levels between groups (false discovery rate 1%, fold change at least twofold). The annotation of the significantly changing transcripts derived from the Bovine Genome Array was supplemented based on the current UniGene build #79, Ensembl gene IDs, and BLAST analyses. In comparison of the groups AI vs. CPH 460 mRNAs, AI vs. CPL 1340 mRNAs, and CPH vs. CPL 1370 mRNAs were obtained that met the significance threshold. The identified genes were assigned to Gene Ontology categories and to molecular pathways for each comparison. Most specific categories and pathways were investigated in more detail (e.g. using literature-based networks) to find molecular functions that are specifically regulated by progesterone or by embryonic signaling.