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Genome-Wide Analysis of MicroRNA-related Single Nucleotide Polymorphisms (SNPs) in Mouse Genome
Gideon Omariba1, Fuyi Xu1,2, Maochun Wang1
1College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China.
Abstract:
MicroRNAs are widely referred to as gene expression regulators for different diseases. The integration between single nucleotide polymorphisms (SNPs) and miRNAs has been associated with both human and animal diseases. In order to gain new insights on the effects of SNPs on miRNA and their related sequences, we steadily characterized a whole mouse genome miRNA related SNPs, analyzed their effects on the miRNA structural stability and target alteration. In this study, we collected 73643859 SNPs across the mouse genome, analyzed 1187 pre-miRNAs and 2027 mature miRNAs. Upon mapping the SNPs, 1700 of them were identified in 702 pre-miRNAs and 609 SNPs in mature miRNAs. We also discovered that SNP densities of the pre-miRNA and mature miRNAs are lower than the adjacent flanking regions. Also the flanking regions far away from miRNAs appeared to have higher SNP density. In addition, we also found that transitions were more frequent than transversions in miRNAs. Notably, 841 SNPs could change their corresponding miRNA's secondary structure from stable to unstable. We also performed target gain and loss analysis of 163 miRNAs and our results showed that few miRNAs remained unchanged and many miRNAs from wild mice gained target site. These results outline the first case of SNP variations in the mouse whole genome scale. Those miRNAs with changes in structure or target could be of interest for further studies.
Insights
Single nucleotide polymorphisms (SNPs) in mouse genomes affect microRNA (miRNA) stability and gene targets. This study provides the first whole-genome analysis of miRNA-associated SNPs, revealing their impact on miRNA structure and function.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- MicroRNAs (miRNAs) are key regulators of gene expression implicated in various diseases.
- Single nucleotide polymorphisms (SNPs) interacting with miRNAs are linked to both human and animal diseases.
- Understanding SNP effects on miRNA structure and function is crucial for disease research.
Purpose of the Study:
- To comprehensively characterize miRNA-related SNPs across the entire mouse genome.
- To analyze the impact of these SNPs on miRNA structural stability and target gene interactions.
- To provide novel insights into the functional consequences of genetic variations in miRNA sequences.
Main Methods:
- Collected and analyzed 73,643,859 SNPs from the mouse genome.
- Mapped SNPs to 1187 pre-miRNAs and 2027 mature miRNAs.
- Evaluated SNP effects on miRNA secondary structure and performed target gain/loss analysis.
Main Results:
- Identified 1700 SNPs in pre-miRNAs and 609 SNPs in mature miRNAs.
- Observed lower SNP densities within miRNAs compared to flanking regions.
- Found that 841 SNPs destabilized miRNA secondary structures, and many gained target sites.
Conclusions:
- This study presents the first whole-genome-scale analysis of SNP variations associated with miRNAs in mice.
- Identified SNPs significantly alter miRNA structural stability and target repertoire.
- These structurally or functionally altered miRNAs represent potential candidates for future disease-related investigations.
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