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BMC Genomics. 2013 Sep 10;14:609. doi: 10.1186/1471-2164-14-609.

Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species.

Author information

1
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada. lguan@ualberta.ca.

Abstract

BACKGROUND:

Understanding how species-specific microRNAs (miRNAs) contribute to species-specific phenotypes is a central topic in biology. This study aimed to elucidate the role of ruminant-specific miRNAs in shaping mRNA expression divergence between ruminant and non-ruminant species.

RESULTS:

We analyzed miRNA and mRNA transcriptomes generated by Illumina sequencing from whole blood samples of cattle and a closely related non-ruminant species, pig. We found evidence of expansion of cattle-specific miRNAs by analyzing miRNA conservation among 57 vertebrate species. The emergence of cattle-specific miRNAs was accompanied by accelerated sequence evolution at their target sites. Further, the target genes of cattle-specific miRNAs show markedly reduced expression compared to their pig and human orthologues. We found that target genes with conserved or non-conserved target sites of cattle-specific miRNAs exhibit reduced expression. One of the significantly enriched KEGG pathway terms for the target genes of the cattle-specific miRNAs is the insulin signalling pathway, raising the possibility that some of these miRNAs may modulate insulin resistance in ruminants.

CONCLUSIONS:

We provide evidence of rapid miRNA-mediated regulatory evolution in the ruminant lineage. Cattle-specific miRNAs play an important role in shaping gene expression divergence between ruminant and non-ruminant species, by influencing the expression of targets genes through both conserved and cattle-specific target sites.

PMID:
24020371
PMCID:
PMC3847189
DOI:
10.1186/1471-2164-14-609
[Indexed for MEDLINE]
Free PMC Article

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