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During the early stages of pregnancy, the uterine endometrium undergoes dramatic morphologic and functional changes accompanied with dynamic variation in gene expression. Pregnancy-stage specific differentially expressed gene (DEG)-transcript-probes were investigated and identified by comparing endometrium transcriptome at 9th day (9D), 12th day (12D) and 16th day (16D) of early pregnancy in Polish large-white (PLW) gilts. Endometrium comparisons between 9D-vs-12D, 9D-vs-16D and 12D-vs-16D of early pregnancy identified 6049, 374 and 6034 highly significant DEG-transcript-probes (<i>p</i> < 0.001; >2 FC). GO term enrichment analysis identified commonly shared upregulated endometrial DEG-transcript-probes (<i>p</i> < 0.001; >2 FC), that were regulating the gene functions of anatomic structure development and transport (<i>TG</i>), DNA-binding and <i>methyltransferase</i> activity (<i>ZBTB2</i>), ion-binding and <i>kinase</i> activity (<i>CKM</i>), cell proliferation and apoptosis activity (<i>IL1B)</i>. Downregulated DEG-transcript-probes (<i>p</i> < 0.001; >2 FC) were involved in regulating the gene functions of <i>phosphatase</i> activity (<i>PTPN11</i>), TC616413 gene-transcript and <i>Sus-scrofa</i> LOC100525539. Moreover, blastn comparison of microarray-probes sequences against <i>sus-scrofa11</i> assembly identified commonly shared upregulated endometrial DEG-transcript-probes (E < 0.06; >2 FC), that were regulating the gene functions of reproduction and growth (<i>SELENOP</i>), cytoskeleton organization and <i>kinase</i> activity (<i>CDC42BPA</i>), <i>phosphatase</i> activity (<i>MINPP1</i>), enzyme-binding and cell-population proliferation (VAV3), cancer-susceptibility candidate gene (<i>CASC4</i>), cytoskeletal protein-binding (<i>COBLL1</i>), ion-binding, enzyme regulator activity (<i>ACAP2</i>) Downregulated endometrial DEG-transcript-probes (E < 0.06; >2FC) were involved in regulating the gene functions of signal-transduction (<i>TMEM33),</i> catabolic and metabolic processes (<i>KLHL15)</i>. Microarray validation experiment on selected candidate genes showed complementarity to significant endometrial DEG-transcript-probes responsible for the regulation of immune response (<i>IL1B, S100A11</i>), lipid metabolism (<i>FABP3, PPARG</i>), cell-adhesion (<i>ITGAV</i>), <i>angiogenesis</i> (<i>IL1B</i>), intercellular transmission (<i>NMB</i>), cell-adhesion (<i>OPN</i>) and response to stimuli (<i>RBP4</i>) was confirmed by RT-PCR. This study provides a clue that identified pregnancy-stage specific microarray transcript probes could be considered as candidate genes for recognition and establishment of early pregnancy in the pig.