{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:34:12Z","timestamp":1790210052999,"version":"4.1.0"},"reference-count":43,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:00:00Z","timestamp":1781740800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell Dev. Biol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      RNA-seq analysis followed by TMM normalization and voom\u2013limma modeling identified differential expression in both compartments. Differential expression was defined by an adjusted P-value (FDR threshold &amp;lt;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 &amp;gt;1. Gene-level interpretation was restricted to transcripts with a Bayesian posterior probability of differential expression (B &amp;gt; 1). In the conceptus, high-confidence upregulated genes from day 8 to 12 included steroidogenic enzymes (\n                      <jats:italic>CYP19A1, CYP17A1<\/jats:italic>\n                      ), extracellular matrix components (\n                      <jats:italic>COL4A1, COL4A2, COL4A5, SPON1, DSG2<\/jats:italic>\n                      ), protease regulators (\n                      <jats:italic>SERPINE1, TMPRSS2, LGMN<\/jats:italic>\n                      ), and selective transporters (\n                      <jats:italic>AQP5, SLC2A5, ATP1B3<\/jats:italic>\n                      ). In the endometrium, downregulated genes in pregnant mares included immediate-early transcriptional regulators (\n                      <jats:italic>EGR1, FOS, DUSP1<\/jats:italic>\n                      ) and oxidative stress\u2013associated genes (\n                      <jats:italic>GSTA4<\/jats:italic>\n                      ), while upregulated genes in pregnant mares included signaling and regulatory components (\n                      <jats:italic>HRAS, PUM3, U2AF1L4, COPS6<\/jats:italic>\n                      ), complement regulator\n                      <jats:italic>C4BPA<\/jats:italic>\n                      , and mitochondrial sulfide metabolism gene\n                      <jats:italic>SQOR<\/jats:italic>\n                      . Functional enrichment analysis supported coordinated extracellular matrix organization and signaling modulation without enrichment of inflammatory pathways.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>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\u2013maternal communication that precedes the classical maternal recognition phase and is consistent with early embryo\u2013maternal communication associated with the transition toward maternal recognition.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fcell.2026.1840498","type":"journal-article","created":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T14:58:23Z","timestamp":1781794703000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Matched embryo\u2013endometrium RNA-seq reveals coordinated but asymmetric transcriptomic reprogramming at the onset of early equine pregnancy"],"prefix":"10.3389","volume":"14","author":[{"given":"Eva","family":"Da Silva \u00c1lvarez","sequence":"first","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 M.","family":"Ortiz-Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Department of Veterinary Clinical Sciences, Alma Mater Studiorum, University of Bologna","place":["Bologna, Italy"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco E.","family":"Mart\u00edn-Cano","sequence":"additional","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"\u00c1lvarez-Barrientos","sequence":"additional","affiliation":[{"name":"Service of Techniques Applied to Biosciences, University of Extremadura","place":["Badajoz, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Becerro-Rey","sequence":"additional","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda C.","family":"Gil","sequence":"additional","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eloy","family":"Redondo","sequence":"additional","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Javier","family":"Masot","sequence":"additional","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"In\u00e9s M.","family":"Aparicio","sequence":"additional","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando J.","family":"Pe\u00f1a","sequence":"additional","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Ortega-Ferrusola","sequence":"additional","affiliation":[{"name":"Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura","place":["C\u00e1ceres, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,6,18]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/s40104-015-0048-6","article-title":"Early pregnancy in the horse revisited - does exception prove the rule?","volume":"6","author":"Aurich","year":"2015","journal-title":"J. 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