Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition.

Seungwoo Lee,Dayoung Oh,Seungwoo Hwang,Hee Jeong Yu,Yu Jung Choi,Yongbaek Kim,Myung-Chul Kim,Doug-Young Ryu,Turgay Unver

doi:10.1371/journal.pone.0146374

Seungwoo Lee, Dayoung Oh + Show 7 more

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https://doi.org/10.1371/journal.pone.0146374

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Abstract

MicroRNAs (miRNAs) in blood plasma are stable under high levels of ribonuclease activity and could function in tissue-to-tissue communication, suggesting that they may have distinctive structural characteristics compared with non-circulating miRNAs. In this study, the expression of miRNAs in horse plasma and their characteristic nucleotide composition were examined and compared with non-plasma miRNAs. Highly expressed plasma miRNA species were not part of the abundant group of miRNAs in non-plasma tissues, except for the eca-let-7 family. eca-miR-486-5p, -92a, and -21 were among the most abundant plasma miRNAs, and their human orthologs also belong to the most abundant group of miRNAs in human plasma. Uracil and guanine were the most common nucleotides of both plasma and non-plasma miRNAs. Cytosine was the least common in plasma and non-plasma miRNAs, although levels were higher in plasma miRNAs. Plasma miRNAs also showed higher expression levels of miRNAs containing adenine and cytosine repeats, compared with non-plasma miRNAs. These observations indicate that miRNAs in the plasma have a unique nucleotide composition.

Highlights

MicroRNAs represent a class of small (~22 nt) noncoding RNAs, which regulate gene expression by binding to specific mRNA targets and promoting their degradation and/or translational inhibition [1, 2]. miRNAs recognize many mRNAs with partial complementarity, mostly involving a “seed” region that encompasses residues 2–8 from the 50-end, or 502–508.The genome of the horse (Equus caballus) has 64 chromosomes (2n = 64) containing 2.7 Gb with 20,000 protein-coding genes [3]
Generation sequencing-based small RNA profiles were generated for three horse plasma libraries (Table 1), with 21.8–25.6 million sequencing reads obtained from each library
Uracil was the most frequent nucleotide identified at both ends of miRNAs where guanine and cytosine were under-represented (Fig 5); this has previously been reported [9, 13], suggesting that similarities exist between the nucleotide composition of horse miRNAs and those of other animals

Summary

Introduction

MicroRNAs (miRNAs) represent a class of small (~22 nt) noncoding RNAs, which regulate gene expression by binding to specific mRNA targets and promoting their degradation and/or translational inhibition [1, 2]. MiRNAs recognize many mRNAs with partial complementarity, mostly involving a “seed” region that encompasses residues 2–8 from the 50-end, or 502–508. The genome of the horse (Equus caballus) has 64 chromosomes (2n = 64) containing 2.7 Gb with 20,000 protein-coding genes [3]. 690 mature horse miRNA species have been identified (http://www.mirbase.org/, accessed May 2015) in various tissues including the liver, colon, muscle, cartilage, subchondral bone, and ovarian follicle as well as cord blood-derived mesenchymal stromal cells [4,5,6,7,8].

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