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MicroRNA sequence variation can impact interactions with target mRNA in cattle

文献类型： 外文期刊

作者： Hao, Dan 1 ; Wang, Xiao 3 ; Yang, Yu 2 ; Chen, Hong 2 ; Thomsen, Bo 1 ; Holm, Lars-Erik 1 ;

作者机构： 1.Aarhus Univ, Dept Mol Biol & Genet, DK-8000 Aarhus C, Denmark

2.Northwest A&F Univ, Coll Anim Sci & Technol, Shaanxi Key Lab Anim Genet Breeding & Reprod Shaan, Yangling 712100, Shaanxi, Peoples R China

3.Shandong Acad Agr Sci, Inst Anim Sci & Vet Med, Jinan 250100, Peoples R China

4.Konge Larsen ApS, DK-2800 Lyngby, Denmark

关键词： Cattle; MicroRNA; Single -nucleotide polymorphism; Quantitative trait locus

期刊名称：GENE （ 影响因子：3.5； 五年影响因子：3.3 ）

ISSN： 0378-1119

年卷期： 2023 年 868 卷

页码：

收录情况： SCI

摘要： Background: 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 wholegenome re-sequencing datasets of 1632 cattle of five breeds from the 1000 bull genomes project.Results: 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. Conclusion: 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.

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