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Updated: May 19, 2026
MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method
Published on: October 7, 2025
Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs
Ya-Ping Zhu1, Wei Xue, Jin-Tu Wang
1The Centre for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing 100141, China.
Background:
MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRNA regulation as well as to alter miRNA biogenesis. SNPs are often associated with diseases or traits. To date, no studies into the effects of SNPs on miRNA biogenesis and regulation in the common carp have been reported.
Results:
Using homology-based prediction combined with small RNA sequencing, we have identified 113 common carp mature miRNAs, including 92 conserved miRNAs and 21 common carp specific miRNAs. The conserved miRNAs had significantly higher expression levels than the specific miRNAs. The miRNAs were clustered into three phylogenetic groups. Totally 394 potential miRNA binding sites in 206 target mRNAs were predicted for 83 miRNAs. We identified 13 SNPs in the miRNA precursors. Among them, nine SNPs had the potential to either increase or decrease the energy of the predicted secondary structures of the precursors. Further, two SNPs in the 3' untranslated regions of target genes were predicted to either disturb or create miRNA-target interactions.
Conclusions:
The common carp miRNAs and their target genes reported here will help further our understanding of the role of miRNAs in gene regulation. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The resource data generated in this study will help advance the study of miRNA function and phenotype-associated miRNA identification.
Insights
Researchers identified 113 microRNAs (miRNAs) in common carp, including 21 novel ones. They also found single-nucleotide polymorphisms (SNPs) affecting miRNA regulation and biogenesis, offering insights into gene regulation and trait association.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- MicroRNAs (miRNAs) are crucial for post-transcriptional gene regulation across diverse organisms.
- miRNA targets and the impact of genetic variations like single-nucleotide polymorphisms (SNPs) on miRNA function remain largely unexplored in common carp.
- Previous studies in model species indicate SNPs can significantly alter miRNA biogenesis and regulatory activity, often correlating with traits or diseases.
Purpose of the Study:
- To identify and characterize microRNAs (miRNAs) in the common carp.
- To predict potential miRNA targets and analyze miRNA-related single-nucleotide polymorphisms (SNPs).
- To investigate the effects of identified SNPs on miRNA biogenesis and target interactions in common carp.
Main Methods:
- Homology-based prediction and small RNA sequencing were employed to identify common carp miRNAs.
- Bioinformatic tools were used to predict miRNA binding sites in target messenger RNAs (mRNAs).
- Analysis of single-nucleotide polymorphisms (SNPs) within miRNA precursors and target gene regions was performed.
Main Results:
- 113 mature miRNAs were identified, comprising 92 conserved and 21 common carp-specific miRNAs, with conserved miRNAs showing higher expression.
- 394 potential miRNA binding sites were predicted across 206 target mRNAs for 83 miRNAs.
- 13 SNPs were found in miRNA precursors, with nine potentially altering secondary structure stability; two SNPs in target gene 3' UTRs were predicted to affect miRNA binding.
Conclusions:
- The identified common carp miRNAs and their targets provide a foundational resource for understanding miRNA-mediated gene regulation in this species.
- The study offers novel insights into how SNPs can influence miRNA biogenesis and function, with implications for trait and disease association studies.
- Generated data will facilitate future research on miRNA function and the identification of phenotype-associated miRNAs in common carp.
