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Updated: May 10, 2026
MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method
Published on: October 7, 2025
Genome-wide and species-wide in silico screening for intragenic MicroRNAs in human, mouse and chicken
Irena Godnic1, Minja Zorc, Dasa Jevsinek Skok
1Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia.
Abstract:
MicroRNAs (miRNAs) are non-coding RNAs (ncRNAs) involved in regulation of gene expression. Intragenic miRNAs, especially those exhibiting a high degree of evolutionary conservation, have been shown to be coordinately regulated and/or expressed with their host genes, either with synergistic or antagonistic correlation patterns. However, the degree of cross-species conservation of miRNA/host gene co-location is not known and co-expression information is incomplete and fragmented among several studies. Using the genomic resources (miRBase and Ensembl) we performed a genome-wide in silico screening (GWISS) for miRNA/host gene pairs in three well-annotated vertebrate species: human, mouse, and chicken. Approximately half of currently annotated miRNA genes resided within host genes: 53.0% (849/1,600) in human, 48.8% (418/855) in mouse, and 42.0% (210/499) in chicken, which we present in a central publicly available Catalog of intragenic miRNAs (http://www.integratomics-time.com/miR-host/catalog). The miRNA genes resided within either protein-coding or ncRNA genes, which include long intergenic ncRNAs (lincRNAs) and small nucleolar RNAs (snoRNAs). Twenty-seven miRNA genes were found to be located within the same host genes in all three species and the data integration from literature and databases showed that most (26/27) have been found to be co-expressed. Particularly interesting are miRNA genes located within genes encoding for miRNA silencing machinery (DGCR8, DICER1, and SND1 in human and Cnot3, Gdcr8, Eif4e, Tnrc6b, and Xpo5 in mouse). We furthermore discuss a potential for phenotype misattribution of miRNA host gene polymorphism or gene modification studies due to possible collateral effects on miRNAs hosted within them. In conclusion, the catalog of intragenic miRNAs and identified 27 miRNA/host gene pairs with cross-species conserved co-location, co-expression, and potential co-regulation, provide excellent candidates for further functional annotation of intragenic miRNAs in health and disease.
Insights
This study identifies intragenic microRNAs (miRNAs) conserved across species, revealing that many reside within host genes and are co-expressed. The findings offer insights into miRNA regulation and potential impacts on gene studies.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- MicroRNAs (miRNAs) are key regulators of gene expression.
- Intragenic miRNAs are often co-regulated with their host genes, but cross-species conservation of this co-location is unknown.
- Existing co-expression data for miRNA/host gene pairs is fragmented.
Purpose of the Study:
- To perform a genome-wide in silico screening for miRNA/host gene pairs across species.
- To assess the cross-species conservation of miRNA/host gene co-location and co-expression.
- To create a catalog of intragenic miRNAs and identify conserved pairs for further functional studies.
Main Methods:
- Genome-wide in silico screening (GWISS) using genomic resources (miRBase, Ensembl).
- Analysis of miRNA/host gene pairs in human, mouse, and chicken.
- Data integration from literature and databases to assess co-expression.
Main Results:
- Approximately half of annotated miRNA genes reside within host genes across species (53% in human, 48.8% in mouse, 42% in chicken).
- A Catalog of intragenic miRNAs was created and is publicly available.
- Twenty-seven miRNA genes showed conserved co-location in all three species, with most (26/27) found to be co-expressed.
Conclusions:
- A significant proportion of miRNA genes are intragenic and conserved across vertebrates.
- The identified 27 conserved miRNA/host gene pairs are strong candidates for functional annotation.
- Polymorphisms or modifications in host genes may have collateral effects on hosted miRNAs, impacting phenotype studies.
