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Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy

1
Department of Animal Genomics and Biodiversity, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzebiec, 05-552 Magdalenka, Poland
2
Wageningen UR Livestock Research, Animal Breeding and Genomics, 6708 PB Wageningen, The Netherlands
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Institute of Biological Bases of Animal Production, Faculty of Biology, Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, 20-950 Lublin, Poland
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Department of Biopharmaceutics and Pharmacodynamics, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland
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Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Toruń, Poland
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Department of Reproduction and Clinic of Farm Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Science, 50-366 Wrocław, Poland
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Department of Biochemistry and Animal Biotechnology, Faculty of Animal Bio-engineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
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Department of Pig Breeding, Faculty of Animal Bio-engineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland
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Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Toruń, Poland
*
Author to whom correspondence should be addressed.
Life 2020, 10(5), 68; https://doi.org/10.3390/life10050068
Received: 22 April 2020 / Revised: 13 May 2020 / Accepted: 13 May 2020 / Published: 16 May 2020
(This article belongs to the Section Animal Science)
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 (p < 0.001; >2 FC). GO term enrichment analysis identified commonly shared upregulated endometrial DEG-transcript-probes (p < 0.001; >2 FC), that were regulating the gene functions of anatomic structure development and transport (TG), DNA-binding and methyltransferase activity (ZBTB2), ion-binding and kinase activity (CKM), cell proliferation and apoptosis activity (IL1B). Downregulated DEG-transcript-probes (p < 0.001; >2 FC) were involved in regulating the gene functions of phosphatase activity (PTPN11), TC616413 gene-transcript and Sus-scrofa LOC100525539. Moreover, blastn comparison of microarray-probes sequences against sus-scrofa11 assembly identified commonly shared upregulated endometrial DEG-transcript-probes (E < 0.06; >2 FC), that were regulating the gene functions of reproduction and growth (SELENOP), cytoskeleton organization and kinase activity (CDC42BPA), phosphatase activity (MINPP1), enzyme-binding and cell-population proliferation (VAV3), cancer-susceptibility candidate gene (CASC4), cytoskeletal protein-binding (COBLL1), ion-binding, enzyme regulator activity (ACAP2) Downregulated endometrial DEG-transcript-probes (E < 0.06; >2FC) were involved in regulating the gene functions of signal-transduction (TMEM33), catabolic and metabolic processes (KLHL15). Microarray validation experiment on selected candidate genes showed complementarity to significant endometrial DEG-transcript-probes responsible for the regulation of immune response (IL1B, S100A11), lipid metabolism (FABP3, PPARG), cell-adhesion (ITGAV), angiogenesis (IL1B), intercellular transmission (NMB), cell-adhesion (OPN) and response to stimuli (RBP4) 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. View Full-Text
Keywords: upregulated; downregulated; differentially expressed genes; transcripts; fold change; preimplantation; embryo; pregnancy; microarray; porcine; endometrium upregulated; downregulated; differentially expressed genes; transcripts; fold change; preimplantation; embryo; pregnancy; microarray; porcine; endometrium
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Pierzchała, M.; Pierzchała, D.; Ogłuszka, M.; Poławska, E.; Blicharski, T.; Roszczyk, A.; Nawrocka, A.; Urbański, P.; Stepanow, K.; Ciepłoch, A.; Korwin-Kossakowska, A.; te Pas, M.F.; Slaska, B.; Buszewska-Forajta, M.; Jaśkowski, J.M.; Sachajko, M.; Herudzińska, M.; Jaśkowski, B.M.; Niżański, W.; Fraser, L.; Czarnik, U.; Kadarmideen, H.N.; Pareek, C.S. Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy. Life 2020, 10, 68.

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