Matched embryo-endometrium RNA-seq reveals coordinated but asymmetric transcriptomic reprogramming at the onset of...

Maternal recognition of pregnancy (MRP) in the mare requires coordinated adaptations of both the conceptus and the endometrium during the peri-recognition interval; however, integrated transcriptomic analyses of both compartments within the same biological window remain limited. Here, we analyzed conceptus RNA-seq data across embryonic age (Days 8 and 12 post ovulation) and endometrial RNA-seq data across pregnancy status (pregnant versus non-pregnant mares sampled between Days 8 and 12 post ovulation). In pregnant mares, conceptus recovery and endometrial biopsy collection were performed within the same gestation, allowing biological integration of embryo and maternal transcriptomes while preserving tissue-specific statistical contrasts.

RNA-seq analysis followed by TMM normalization and voom-limma modeling identified differential expression in both compartments. Differential expression was defined by an adjusted P-value (FDR threshold <0.001). The B-statistic (log-odds of differential expression) was used to prioritize high-confidence candidates for interpretation and downstream modeling, considering genes with a Bayesian posterior probability >1. Gene-level interpretation was restricted to transcripts with a Bayesian posterior probability of differential expression (B > 1). In the conceptus, high-confidence upregulated genes from day 8 to 12 included steroidogenic enzymes (CYP19A1, CYP17A1), extracellular matrix components (COL4A1, COL4A2, COL4A5, SPON1, DSG2), protease regulators (SERPINE1, TMPRSS2, LGMN), and selective transporters (AQP5, SLC2A5, ATP1B3). In the endometrium, downregulated genes in pregnant mares included immediate-early transcriptional regulators (EGR1, FOS, DUSP1) and oxidative stress-associated genes (GSTA4), while upregulated genes in pregnant mares included signaling and regulatory components (HRAS, PUM3, U2AF1L4, COPS6), complement regulator C4BPA, and mitochondrial sulfide metabolism gene SQOR. Functional enrichment analysis supported coordinated extracellular matrix organization and signaling modulation without enrichment of inflammatory pathways.

Matched transcriptomic profiling reveals coordinated but compartment-specific gene regulation at the onset of early equine pregnancy. The conceptus exhibits endocrine and interface specialization, whereas the endometrium demonstrates attenuation of immediate-early transcriptional programs and selective signaling recalibration. These data define a high-confidence systems-level framework for early embryo-maternal communication that precedes the classical maternal recognition phase and is consistent with early embryo-maternal communication associated with the transition toward maternal recognition.