Hao Dan, Wang Xiao, Yang Yu, Chen Hong, Thomsen Bo, Holm Lars-Erik
Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark; College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, 712100 Yangling, Shaanxi, China.
Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, 250100 Jinan, China; Konge Larsen ApS, 2800 Kongens Lyngby, Denmark.
Gene. 2023 Jun 5;868:147373. doi: 10.1016/j.gene.2023.147373. Epub 2023 Mar 17.
Small non-coding microRNAs (miRNAs) are important modulators at post-transcriptional levels. Single-nucleotide polymorphisms (SNPs) located in miRNA genes can alter the secondary structure of pre-miRNA to either impair or promote the miRNA maturation processes. Furthermore, SNPs located in the miRNA seed regions can stabilize or disturb miRNA-target interactions, thereby, quantitatively influence the expression of target genes. Therefore, the main objective of this study was to detect SNPs in bovine miRNAs using the whole-genome re-sequencing datasets of 1632 cattle of five breeds from the 1000 bull genomes project.
In total, our study identified 1109, 334, and 130 SNPs in the miRNA precursor, mature, and seed regions, respectively. The heterozygosity values were generally less than 0.3, and the minor allele frequencies (MAFs) were mainly less than 0.1. Most SNPs were in Hardy-Weinberg equilibrium (HWE) (HWE-P > 0.05). Furthermore, we found that the majority of SNPs (MAF > 0.1 and HWE-P > 0.05) in the miRNA seed regions altered the repertoire of target genes, which in turn were enriched in different KEGG pathways or GO terms. Thus target prediction for bta-miR-2888 revealed loss of 309 target genes and gain of 691 target genes. The 691 gained target genes were significantly enriched in 60 KEGG pathways and 21 GO terms.
In summary, our study identified candidate SNPs in miRNA precursor, mature, and seed regions that are likely to affect target RNA interactions, thereby potentially influencing cattle phenotypic traits.
小型非编码微小RNA（miRNA）是转录后水平的重要调节因子。位于miRNA基因中的单核苷酸多态性（SNP）可改变前体miRNA的二级结构，从而损害或促进miRNA的成熟过程。此外，位于miRNA种子区域的SNP可稳定或干扰miRNA与靶标的相互作用，进而定量影响靶基因的表达。因此，本研究的主要目的是利用来自1000公牛基因组计划的五个品种1632头牛的全基因组重测序数据集，检测牛miRNA中的SNP。
我们的研究总共在miRNA前体、成熟和种子区域分别鉴定出1109个、334个和130个SNP。杂合度值一般小于0.3，次要等位基因频率（MAF）主要小于0.1。大多数SNP处于哈迪-温伯格平衡（HWE）（HWE-P>0.05）。此外，我们发现miRNA种子区域中的大多数SNP（MAF>0.1且HWE-P>0.05）改变了靶基因库，这些靶基因进而在不同的KEGG途径或GO术语中富集。因此，对bta-miR-2888的靶标预测显示，有309个靶基因丢失，691个靶基因增加。增加的691个靶基因在60条KEGG途径和21个GO术语中显著富集。
总之，我们的研究在miRNA前体、成熟和种子区域鉴定出可能影响靶RNA相互作用的候选SNP，从而可能影响牛的表型性状。
