Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Liver plays an important role in the feed efficiency of animals and high and low efficient cattle demonstrated different gene expression profiles by microarray. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI) and identify miRNAs related to feed efficiency in beef cattle. Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1). We identified 305 known bovine miRNAs. Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378, and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (v. 21). We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle. Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI give some insights into liver miRNAs regulating physiological pathways underlying variation in this measure of feed efficiency in bovines.
Highlights
MicroRNAs are small (~22 nucleotides) noncoding RNA that regulate gene expression by targetSubmitted Jul. 19, 2015; Revised Oct. 10, 2015; Accepted Dec. 14, 2015 messenger RNA in a sequence-specific manner, leading to either translational repression or degradation of targeted transcript
Genome wide association studies have been carried out to identify gene markers associated with residual feed intake (RFI) in beef cattle (Sherman et al, 2009) and more than a hundred single nucleotide polymorphic (SNP) markers have been found associated with variation in RFI in beef cattle
Profiling bovine miRNAs In order to profile and identify novel and differentiallyexpressed miRNAs in the bovine liver of low and high RFI cattle, two small RNA libraries were constructed by Solexa sequencing
Summary
MicroRNAs (miRNAs) are small (~22 nucleotides) noncoding RNA that regulate gene expression by target. Genome wide association studies have been carried out to identify gene markers associated with RFI in beef cattle (Sherman et al, 2009) and more than a hundred single nucleotide polymorphic (SNP) markers have been found associated with variation in RFI in beef cattle. Gene expression studies in cattle from high and low RFI divergent selection lines identified more than 160 differentially expressed genes (Chen et al, 2011). We profiled miRNAs abundance in liver tissue of Angus bulls from high and low RFI-selection lines by next-generation deep sequencing technology. We report liver miRNA-seq profiling study in beef cattle and their known and putative novel bovine miRNAs. We report the differentially expressed miRNAs between high and low RFI-selection line cattle
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