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MicroRNA sequence variation can impact interactions with target mRNA in cattle.

Dan Hao1, Xiao Wang2, Yu Yang3

  • 1Department 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.

Gene
|March 19, 2023
PubMed
Summary
This summary is machine-generated.

Single-nucleotide polymorphisms (SNPs) in bovine microRNAs (miRNAs) were identified, potentially impacting gene regulation and cattle traits. These genetic variations in miRNA seed regions alter target gene interactions and associated biological pathways.

Keywords:
CattleMicroRNAQuantitative trait locusSingle-nucleotide polymorphism

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) are small non-coding RNAs regulating gene expression post-transcriptionally.
  • Single-nucleotide polymorphisms (SNPs) in miRNA genes can affect miRNA maturation and target interactions.
  • SNPs in miRNA seed regions can quantitatively influence target gene expression.

Purpose of the Study:

  • To detect single-nucleotide polymorphisms (SNPs) in bovine microRNAs (miRNAs).
  • To analyze the impact of these SNPs on miRNA maturation and target gene interactions.
  • To utilize whole-genome re-sequencing data from the 1000 Bull Genomes Project.

Main Methods:

  • Whole-genome re-sequencing data analysis of 1632 cattle from five breeds.
  • Identification and characterization of SNPs in miRNA precursor, mature, and seed regions.
  • Target gene prediction and enrichment analysis (KEGG pathways, GO terms).

Main Results:

  • 1109, 334, and 130 SNPs identified in miRNA precursor, mature, and seed regions, respectively.
  • Most identified SNPs were in Hardy-Weinberg equilibrium with low heterozygosity and minor allele frequencies.
  • SNPs in seed regions significantly altered target gene repertoires, with bta-miR-2888 showing gain/loss of numerous targets enriched in specific pathways.

Conclusions:

  • Candidate SNPs in bovine miRNA regions were identified.
  • These SNPs are likely to affect miRNA-target interactions.
  • The identified SNPs may influence cattle phenotypic traits.