Construction of protein–protein interaction network based on transcriptome profiling of ovine granulosa cells during the sheep’s anestrus phase
Small antral follicles as the final reserve of folliculogenesis, are existed throughout the reproductive life span of sheep. However, the ovarian cycles of ewe cease in the anestrus phase. This study in thus was aimed to elucidate the ovarian small antral follicles transcriptome in the ewe’s anestrus phase.
Granulosa cells of small antral follicles (#3 mm) were collected from ovaries of anestrous ewes under long days of summer in the non-breeding season as anestrus phase. Transcriptome profiling of these granulosa cells were obtained using the RNA-Seq technology. An integrative analysis was utilized to identify key regulatory genes whose may have potential impacts on intra-ovarian molecular activities.
Globally, 14506 genes were expressed whose higher expressions were belonged to genes that encoded ribosomal proteins. Top significant terms of gene ontology were pertained to protein translational processes. Apart of this, most of highly significant terms were also relevant to apoptotic process through extracellular vesicles, including apoptotic bodies and exosomes. Regarding to node effect property, UBA52 (ubiquitin A-52 residue ribosomal protein fusion product 1) and RPS5 (ribosomal proteins S5) contained in highest out-degree and in-degree, respectively.
Our data suggest that ribosomal mRNA/proteins could make the granulosa cells undergo a lot of changes from the point of view that ovarian activities are ceased in the anestrus phase.
KeywordsRNA-sequencing ovarian follicles anestrus phase protein-protein interaction network functional modules
Unable to display preview. Download preview PDF.
R.T. would like to special thanks to the Dr. Stéphane Fabre, PhD–HDR in INRA research center in Castanet-Tolosan, France, and the staff of the GeT-Genotoul genomic platform (https://doi.org/get/genotoul.fr) for the RNA sequencing, and Sarah Maman of the INRA Sigenae bioinformatics team for Galaxy support. R.T. also thanks Julien Sarry, technician assistance from INRA-GenPhySE research center in Castanet-Tolosan, France, for prepared the RNAseq libraries. Authors wanted to thank Dr. Abbas Farahavar, PhD in Bu-Ali Sina University of Hamedan, Iran, due to his assistances in collecting the mural granulosa cell. This work has been supported by a PhD grant from “Bu-Ali Sina University” and “Agricultural Biotechnology Research Institute” from Iran.
- Bonnet A, Cabau C, Bouchez O, Sarry J, Marsaud N, Foissac S, Woloszyn F, Mulsant P, Mandon-Pepin B (2013). An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog. BMC Genomics, 14(1): 904CrossRefPubMedPubMedCentralGoogle Scholar
- Copois V, Bibeau F, Bascoul-Mollevi C, Salvetat N, Chalbos P, Bareil C, Candeil L, Fraslon C, Conseiller E, Granci V, Mazière P, Kramar A, Ychou M, Pau B, Martineau P, Molina F, Del Rio M (2007). Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J Biotechnol, 127(4): 549–559CrossRefPubMedGoogle Scholar
- Hafez E (1952). Studies on the breeding season and reproduction of the ewe Part I. The breeding season in different environments Part II. The breeding season in one locality. J Agric Sci, 42(03): 189–231Google Scholar
- Holm S (1979). A simple sequentially rejective multiple test procedure. Scand J Stat, 6): 65–70Google Scholar
- Kobayashi M, Oshima S, Maeyashiki C, Nibe Y, Otsubo K, Matsuzawa Y, Nemoto Y, Nagaishi T, Okamoto R, Tsuchiya K, Nakamura T, Watanabe M (2016). The ubiquitin hybrid gene UBA52 regulates ubiquitination of ribosome and sustains embryonic development. Sci Rep, 6(1): 36780CrossRefPubMedPubMedCentralGoogle Scholar
- Romereim S M, Summers A F, Pohlmeier W E, Zhang P, Hou X, Talbott H A, Cushman R A, Wood J R, Davis J S, Cupp A S (2017). Gene expression profiling of bovine ovarian follicular and luteal cells provides insight into cellular identities and functions. Mol Cell Endocrinol, 439): 379–394CrossRefPubMedGoogle Scholar
- Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou K P, Kuhn M, Bork P, Jensen L J, von Mering C (2015). STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Res, 43(Database issue): D447–D452CrossRefPubMedGoogle Scholar
- Trapnell C, Williams B A, Pertea G, Mortazavi A, Kwan G, van BarenM J, Salzberg S L,Wold B J, Pachter L (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 28(5): 511–515CrossRefPubMedPubMedCentralGoogle Scholar
- Vizirianakis I S, Papachristou E T, Andreadis P, Zopounidou E, Matragkou C N, Tsiftsoglou A S (2015). Genetic manipulation of RPS5 gene expression modulates the initiation of commitment of MEL cells to erythroid maturation: Implications in understanding ribosomopathies. Int J Oncol, 47(1): 303–314CrossRefPubMedGoogle Scholar