Abstract
MicroRNAs are short (17–24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. In recent years, deep sequencing of the transcriptome is increasingly being utilized with the promise of higher sensitivity for the identification of differential expression patterns as well as the opportunity to discover new transcripts, including new alternative isoforms and miRNAs. Here, we utilized RNA-seq technology to perform a genome-wide analysis of miRNAs from the adipose tissue of the two species of sheep to look for clues that might explain the fat deposition differences between the sheep. The RNA-seq analysis detected 3132 miRNAs from the adipose tissue of the Small-tail Han and Dorset sheep, of which 2893 were defined as potential new miRNAs. In addition, 54 miRNAs were differentially expressed between the two breeds of sheep. Gene ontology and pathway analyses of the predicted target genes that negatively associated with the differentially expressed miRNAs revealed that there was less active lipid metabolism in the adipose tissue of Small Tail Han sheep. This study can help understand the underling mechanisms responsible for the morphological differences related to fat deposition between two breeds of sheep.
Highlights
IntroductionA microRNA (miRNA) is a small non-coding RNA molecule (about 17–24 nucleotides in length) found in plants, animals, and some viruses, which functions in transcriptional and post-transcriptional gene expression regulation by affecting both the stability and the translation of messenger RNAs (mRNA)1,2. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding
A microRNA is a small non-coding RNA molecule found in plants, animals, and some viruses, which functions in transcriptional and post-transcriptional gene expression regulation by affecting both the stability and the translation of messenger RNAs1,2. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts that can be either protein-coding or non-coding
Additional new miRNA prediction procedures were applied on these reads to identify reliable and unique new miRNA species and the results are described
Summary
A microRNA (miRNA) is a small non-coding RNA molecule (about 17–24 nucleotides in length) found in plants, animals, and some viruses, which functions in transcriptional and post-transcriptional gene expression regulation by affecting both the stability and the translation of messenger RNAs (mRNA)1,2. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The fat tissues from two distinctive breeds of livestock sheep (Small Tail Han and Dorset) were profiled by small RNA deep sequencing technology. Significant differences in the fat deposition between these two breeds have spurred increasing interest in the characterization of the genetic profiles of www.nature.com/scientificreports/ These sheep[13,14,15,16]. For a variety of livestock, there are important differences between species that can only be partially explained by digestive process differences[13] This suggests that the factors and mechanisms responsible for the differences in fat deposition, which have not been elucidated completely, could aid in the development of new strategies to modulate fat deposition and improve the nutritional value of meat. The present study aims to examine differentially expressed miRNAs from two species of sheep in order to identify key pathways that might be related to the mechanism of fat deposition using bioinformatics
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