Comprehensive transcriptomic profiling of dynamic endometrial alterations during different implantation stages in goats (Capra hircus)

Abstract The establishment of endometrial receptivity constitutes a multifaceted biological process orchestrated by intricate regulatory networks, representing a critical determinant for successful embryo implantation and pregnancy outcomes. This study systematically characterized the dynamic landscapes of non-coding RNA (ncRNA) and mRNA in the goat endometrium across distinct implantation stages. Endometrial tissues from goats at gestational days 10 (D10, n = 4), 17 (D17, n = 4), and pregnancy failure at gestational day 17 (PF, n = 3) were collected; in addition, three samples from each group (n = 3) were selected for transcriptomic sequencing of mRNA, lncRNA, circRNA, and miRNA. The receptive endometrium (D17) exhibited enhanced glandular development, mature pinopodes, elevated estrogen and progesterone levels, and a reduced estrogen/progesterone ratio, along with upregulated markers (VEGF, OPN, IGF1R). Transcriptome profiling identified 6,104 differentially expressed mRNAs (DEmRNAs), 485 lncRNAs (DElncRNAs), 1,694 circRNAs (DEcircRNAs), and 203 miRNAs (DEmiRNAs) across stages. Functional enrichment analysis highlighted the pivotal roles of MAPK, TNF, and RAS signaling pathways in establishing endometrial receptivity, with hub genes including ISG15, CXCL10, IFI6, and RSAD2 contributing significantly to the development of uterine receptivity in goats. Furthermore, ncRNAs such as MSTRG774.1, novel_circ_000145, novel_circ_000257, and chi-miR-348-3p exhibited specific or elevated expression patterns during the receptive phase, suggesting their potential regulatory functions in maintaining the endometrial receptivity microenvironment. Moreover, an integrated competing endogenous RNA (ceRNA) network was constructed to elucidate potential interactions between ncRNAs and mRNAs, offering novel insights into the molecular regulatory mechanisms underlying endometrial receptivity in ruminants.