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| Status |
Public on Nov 27, 2015 |
| Title |
Characterization and profiling of liver microRNAs in cattle divergently selected for residual feed intake by RNA-sequencing |
| Organism |
Bos taurus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. 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
Results: 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 (miRBase v.19). 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 (version 19). 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
Conclusions: 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 residual feed intake in bovine
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| Overall design |
2 libraries were constructed from pooled RNA extracted from livers of 13 low-RFI animals and 13 high-RFI animals, sequenced by Illumina genome analyser using single-read cluster generation kit v2
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| Contributor(s) |
Al-Husseini W, Chen Y, Gondro C, Herd RM, Gibson JP, Arthur PF |
| Citation(s) |
26954124 |
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| Submission date |
Nov 27, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
WIJDAN AL-HUSSEINI |
| E-mail(s) |
wabedaliune@gmail.com
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| Organization name |
University of New England
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| Department |
Centre for Genetics Analysis and Applications, School of Environmental and Rural Science
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| Street address |
UNE
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| City |
Armidale |
| State/province |
NSW |
| ZIP/Postal code |
2351 |
| Country |
Australia |
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| Platforms (1) |
| GPL11153 |
Illumina Genome Analyzer II (Bos taurus) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA268773 |
| SRA |
SRP050318 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE63691_RAW.tar |
11.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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