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. 2018 Nov 20;8(1):17072.
doi: 10.1038/s41598-018-35315-5.

An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle

Priscila S N De Oliveira  1 , Luiz L Coutinho  2 , Polyana C Tizioto  3 , Aline S M Cesar  2 , Gabriella B de Oliveira  2 , Wellison J da S Diniz  4 , Andressa O De Lima  4 , James M Reecy  5 , Gerson B Mourão  2 , Adhemar Zerlotini  6 , Luciana C A Regitano  7
Affiliations

An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle

Priscila S N De Oliveira et al. Sci Rep. .

Abstract

Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such as bta-miR-486, bta-miR-7, bta-miR15a, bta-miR-21, bta-miR 29, bta- miR-30b, bta-miR-106b, bta-miR-199a-3p, bta-miR-204, and bta-miR 296 may have a potential role in variation of RFI. Functional enrichment analysis of differentially expressed (DE) miRNA's target genes and miRNA-mRNA correlated modules revealed that insulin, lipid, immune system, oxidative stress and muscle development signaling pathways might potentially be involved in RFI in this population. Our study identified DE miRNAs, miRNA - mRNA regulatory networks and hub miRNAs related to RFI. These findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
KEGG insulin signaling pathway identified by WebGestalt from the bta-miR-486 target gene list. Boxes with red labeling indicates target genes for the DE miRNA, while boxes with black labeling are not targeted genes. Solid lines mean direct interaction and dashed lines an indirect interaction between genes.
Figure 2
Figure 2
Co-expression networks of feed efficient group from skeletal muscle (a) and liver (b) in Nelore cattle. Colored diamonds represent the top 5 hub miRNAs within of each module, and colored round rectangles represents the signaling pathways associated (FDR ≤ 0.05) with the genes.
Figure 3
Figure 3
Co-expression networks of feed inefficient group from skeletal muscle (a) and liver (b) in Nelore cattle. Colored diamonds represent the top 5 hub miRNAs of each module, and coloured round rectangles represents the signaling pathways associated (FDR ≤ 0.05) with the genes.
See this image and copyright information in PMC

References

    1. Paradis F., Yue S., Grant J. R., Stothard P., Basarab J. A., Fitzsimmons C. Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers1. Journal of Animal Science. 2015;93(7):3331–3341. doi: 10.2527/jas.2015-8975. - DOI - PubMed
    1. Jing, L. et al. Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs. Sci. Rep., 10.1038/srep11953 (2015). - PMC - PubMed
    1. Al-Husseini Wijdan, Chen Yizhou, Gondro Cedric, Herd Robert M., Gibson John P., Arthur Paul F. Characterization and Profiling of Liver microRNAs by RNA-sequencing in Cattle Divergently Selected for Residual Feed Intake. Asian-Australasian Journal of Animal Sciences. 2015;29(10):1371–1382. doi: 10.5713/ajas.15.0605. - DOI - PMC - PubMed
    1. Coutinho Luiz L., Matukumalli Lakshmi K., Sonstegard Tad S., Van Tassell Curtis P., Gasbarre Louis C., Capuco Anthony V., Smith Timothy P. L. Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues. Physiological Genomics. 2007;29(1):35–43. doi: 10.1152/physiolgenomics.00081.2006. - DOI - PubMed
    1. An Jee Hyun, Ohn Jung Hun, Song Jung Ah, Yang Jae-Yeon, Park Hyojung, Choi Hyung Jin, Kim Sang Wan, Kim Seong Yeon, Park Woog-Yang, Shin Chan Soo. Changes of MicroRNA Profile and MicroRNA-mRNA Regulatory Network in Bones of Ovariectomized Mice. Journal of Bone and Mineral Research. 2014;29(3):644–656. doi: 10.1002/jbmr.2060. - DOI - PubMed

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