Abstract
A total of 31 differentially expressed genes in the mammary glands were identified in our previous study using RNA sequencing (RNA-Seq), for lactating cows with extremely high and low milk protein and fat percentages. To determine the regulation of milk composition traits, we herein investigated the expression profiles of microRNA (miRNA) using small RNA sequencing based on the same samples as in the previous RNA-Seq experiment. A total of 497 known miRNAs (miRBase, release 22.1) and 49 novel miRNAs among the reads were identified. Among these miRNAs, 71 were found differentially expressed between the high and low groups (p < 0.05, q < 0.05). Furthermore, 21 of the differentially expressed genes reported in our previous RNA-Seq study were predicted as target genes for some of the 71 miRNAs. Gene ontology and KEGG pathway analyses showed that these targets were enriched for functions such as metabolism of protein and fat, and development of mammary gland, which indicating the critical role of these miRNAs in regulating the formation of milk protein and fat. With dual luciferase report assay, we further validated the regulatory role of 7 differentially expressed miRNAs through interaction with the specific sequences in 3′UTR of the targets. In conclusion, the current study investigated the complexity of the mammary gland transcriptome in dairy cattle using small RNA-seq. Comprehensive analysis of differential miRNAs expression and the data from previous study RNA-seq provided the opportunity to identify the key candidate genes for milk composition traits.
Highlights
MicroRNAs, which are a class of non-coding small RNA molecules with the length of 18-24 nucleotides, are important regulators of gene expression
The results demonstrated that miR-2904, miR-29c/miR-146b/miR-339a, miR-339b/miR106b/miR-190a down-regulated the expression of the tribbles homolog 3 (TRIB3), M-serum amyloid A3 (SAA3).2 and parathyroid hormone-like hormone (PTHLH), respectively
Using small RNA (sRNA) sequencing, 497 known bovine miRNAs and 49 novel bovine miRNAs were identified in the mammary glands of lactating dairy cows
Summary
MicroRNAs (miRNAs), which are a class of non-coding small RNA (sRNA) molecules with the length of 18-24 nucleotides, are important regulators of gene expression. They can play important roles in a wide range of biological processes, including animal and plant development, cell differentiation, proliferation, apoptosis, and metabolism Many experimental techniques and computational methods have been developed to identify miRNAs (Aravin and Tuschl, 2005; Berezikov et al, 2006a; Landgraf et al, 2007), and large number of miRNAs have been identified in primates, rodents, birds, fish, and plants (Lagos-Quintana et al, 2003; Chen et al, 2005; Finucane et al, 2008; Glazov et al, 2008)
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