Abstract
microRNAs (miRNAs) are important post-transcriptional regulators in eukaryotes that target mRNAs repressing their expression. The uncertain process of pig domestication, with different origin focuses, and the selection process that commercial breeds suffered, have generated a wide spectrum of breeds with clear genetic and phenotypic variability. The aim of this work was to define the miRNAs expression profile in kidney of several porcine breeds. Small RNA libraries from kidney were elaborated and high-throughput sequenced with the 454 Genome Sequencer FLX (Roche). Pigs used were classified into three groups: the European origin group (Iberian breed and European Wild Boar ancestor), European commercial breeds (Landrace, Large White and Piétrain breeds) and breeds with Asian origin (Meishan and Vietnamese breeds). A total of 229 miRNAs were described in the pig kidney miRNA profile, including 110 miRNAs out of the 257 previously described pig miRNAs and 119 orthologous miRNAs. The most expressed miRNAs in pig kidney microRNAome were Hsa-miR-200b-3p, Ssc-miR-125b and Ssc-miR-23b. Moreover, 5 novel porcine miRNAs and 3 orthologous miRNAs could be validated through RT-qPCR. miRNA sequence variation was determined in 116 miRNAs, evidencing the presence of isomiRs. 125 miRNAs were differentially expressed between breed groups. The identification of breed-specific miRNAs, which could be potentially associated to certain phenotypes, is becoming a new tool for the study of the genetic variability underlying complex traits and furthermore, it adds a new layer of complexity to the interesting process of pig evolution.
Highlights
MicroRNAs are small regulatory RNAs that play important roles in the regulation of gene expression [1,2]
Mechanisms involved in isomiRs generation and their biological relevance has increased the complexity of molecular mechanisms related to regulation of messenger RNAs (mRNAs) expression mediated by miRNAs
The percentage of detected miRNAs per breed varied from 55 to 83%, being the Iberian breed the library with less detected miRNAs and the Large White the most, in agreement with the total number of sequences obtained in these libraries
Summary
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in the regulation of gene expression [1,2]. These single-stranded non-coding RNAs that are approximately 22 nucleotides long are involved in post-transcriptional regulation mechanisms acting mainly through down-regulation of target messenger RNAs (mRNAs) in a wide range of biological and pathological processes [3,4]. Mechanisms involved in isomiRs generation and their biological relevance has increased the complexity of molecular mechanisms related to regulation of mRNA expression mediated by miRNAs. Nowadays, a large number of miRNAs have been reported in animals, plants and viruses, with up to 18,226 entries in the miRBase database Several studies showed that variability in miRNA sequences has been lost over time since miRNAs have been described in unicellular eukaryotes, showing its deeper evolutionary history among eukaryotes [18]
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