Novel equine tissue miRNAs and breed-related miRNA expressed in serum

Abstract

BackgroundMiRNAs regulate multiple genes at the post-transcriptional level and therefore play an important role in many biological processes. It has been suggested that miRNA exported outside the cells contribute to inter-cellular communication. Consequently, circulating miRNAs are of particular interest and are promising biomarkers for many diseases. The number of miRNAs annotated in the horse genome is much lower compared to model organisms like human and mouse. We therefore aimed to identify novel equine miRNAs for tissue types and breed in serum.ResultsWe analysed 71 small RNA-seq libraries derived from nine tissues (gluteus medius, platysma, masseter muscle, heart, liver, cartilage, bone, total blood and serum) using miRDeep2 and miRdentify tools. Known miRNAs represented between 2.3 and 62.9 % of the reads in 71 libraries. A total of 683 novel miRNAs were identified. Breed and tissue type affected the number of miRNAs detected and interestingly, affected its average intensity. A total of 50 miRNAs in serum proved to be potential biomarkers to differentiate specific breed types, of which miR-122, miR-200, miR-483 were over-expressed and miR-328 was under-expressed in ponies compared to Warmbloods. The different miRNAs profiles, as well as the differences in their expression levels provide a foundation for more hypotheses based on the novel miRNAs discovered.ConclusionsWe identified 683 novel equine miRNAs expressed in seven solid tissues, blood and serum. Additionally, our approach evidenced that such data supported identification of specific miRNAs as markers of functions related to breeds or disease tissues.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3168-2) contains supplementary material, which is available to authorized users.

Identification of long non-coding RNA in the horse transcriptome

“…Most efforts towards identifying noncoding RNAs has gone to miRNA identification [12–14]. There are, however, over 4,000 lncRNA transcripts predicted by ENSEMBL and NCBI represented in our transcriptome that we have considered as input for our annotation pipeline.…”

MicroRNAs in equine veterinary science

“…Interestingly, certain miRNAs have been shown to be expressed in a tissue‐specific pattern, for example, in equine plasma , which may increase the potential diagnostic and therapeutic applications of miRNAs in the future. MiRNA expression also appears to vary between breeds, with 50 miRNAs identified as potential breed‐specific biomarkers on the basis of differences between the miRNAs detected in the serum of pony breeds and warmblood horse breeds . Significantly, only 33% of the miRNAs expressed in whole blood were also detected in serum , suggesting that the majority of miRNAs detected in whole blood are not exported out of cells.…”

“…MiRNA expression also appears to vary between breeds, with 50 miRNAs identified as potential breed-specific biomarkers on the basis of differences between the miRNAs detected in the serum of pony breeds and warmblood horse breeds [64]. Significantly, only 33% of the miRNAs expressed in whole blood were also detected in serum [64], suggesting that the majority of miRNAs detected in whole blood are not exported out of cells.…”

Profile of Surrounding MicroRNAs in Low Density Lipoprotein Uptake

“…Thus, a new field of miRNA investigations was opened as potential biomarkers for the prognosis and therapeutic targets for the treatment of CVDs. As demonstrate in table 1 [4,13,[16][17][18]. 3 of 13 Tabela1.Surrounding microRNAs related to atherosclerotic process…”

“…It is now known that miRNAs can be synthesized in specific cells and subsequently secreted into plasma, which facilitates the communication between cells of different tissues [13]. The small size of miRNA molecules, and the fact that they are transported into vesicles such as exosomes, microvesicles and lipoproteins, apoptotic bodies and protein complexes, are characteristics that protect these small molecules from the action of plasmatic RNAses and make the microRNAs more stable than mRNAs and DNAs in plasma [14][15].…”