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Identification of Reference Genes for Analysis of microRNA Expression Patterns in Equine Chorioallantoic Membrane and Serum

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Abstract

MicroRNAs (miRNAs) have important posttranscriptional regulatory abilities, and there is considerable interest in evaluating their expression patterns in different pathophysiological states. The most common method of quantifying miRNA expression is quantitative reverse transcription PCR; however, the identification of tissue-specific and species-specific reference miRNA is a prerequisite for miRNA expression analysis. Currently, no reference genes have been described for evaluating miRNA expression in equine serum and chorioallantoic membrane (CAM) during pregnancy. The aim of the present study was to characterize reference genes for normalization of miRNA expression in CAM and serum in the pregnant equine. To identify the most stable miRNAs in serum, expression of potential candidates was evaluated in serum samples from diestrous mares, pregnant mares and geldings. To identify the most stable miRNAs in CAM, expression of potential candidates was evaluated in CAM, collected from mares at 4, 6 and 10 months of pregnancy and immediately postpartum. From a previously generated miRNA sequencing dataset, two separate lists of potential reference miRNAs were identified (serum and CAM) using the NormFinder program, in addition to the commonly used small RNA normalizers, 5S rRNA and U6 snRNA. The putative reference miRNAs were selected using geNorm and NormFinder. In case of a nonsignificant correlation between the results of ranking and stability value between these two programs, ranking from BestKeeper was also included. NormFinder and geNorm consistently identified eca-miR-21-5p, eca-let-7a-5p and eca-miR-10a-5p as the three most stable reference genes for the normalization of serum miRNAs. Within CAM samples, the average ranking obtained from the ranking of NormFinder, geNorm and BestKeeper identified eca-miR-8908a-1-5p, eca-miR-369-5p and eca-miR-106a-5p as the three most stable miRNAs. These observations provide information about equine-specific reference genes that can be used for normalizing miRNAs expression patterns in CAM and serum during the equine pregnancy.

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Acknowledgements

The authors would like to thank Dr. Claudia Klein and Derek Toms for their technical assistance with “SLqPCR” package.

Funding

This work was funded by the Kentucky Thoroughbred Association/Kentucky Thoroughbred Breeders and Owners, the Albert G. Clay Endowment and the Paul Mellon Postdoctoral fellowships at the University of Kentucky and the Special Research Fund (BOF) at Ghent University.

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  1. Department of Veterinary Science, University of Kentucky, Lexington, KY, USA

    Pouya Dini, Shavahn C. Loux, Kirsten E. Scoggin, Alejandro Esteller-Vico, Edward L. Squires, Mats H. T. Troedsson & Barry A. Ball

  2. Department of Reproduction, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium

    Pouya Dini & Peter Daels

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  1. Pouya Dini
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Dini, P., Loux, S.C., Scoggin, K.E. et al. Identification of Reference Genes for Analysis of microRNA Expression Patterns in Equine Chorioallantoic Membrane and Serum. Mol Biotechnol 60, 62–73 (2018). https://doi.org/10.1007/s12033-017-0047-2

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