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Published on: October 7, 2025
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of
Pierre R Bushel1,2, Florian Caiment3, Han Wu4
1Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA.
Abstract:
MicroRNAs (miRNAs) are small RNAs that regulate mRNA expression and have been targeted as biomarkers of organ damage and disease. To explore the utility of miRNAs to assess injury to specific tissues, a tissue atlas of miRNA abundance was constructed. The Rat Atlas of Tissue-specific and Enriched miRNAs (RATEmiRs) catalogues miRNA sequencing data from 21 and 23 tissues in male and female Sprague-Dawley rats, respectively. RATEmiRs identifies tissue-enriched (TE), tissue-specific (TS), or organ-specific (OS) miRNAs via comparisons of one or more tissue or organ vs others. We provide a brief overview of RATEmiRs and present how to use it to detect miRNA expression abundance of candidate biomarkers as well as to compare the expression of miRNAs between rat and human. The database is available at https://www.niehs.nih.gov/ratemirs/.
Insights
The Rat Atlas of Tissue-specific and Enriched miRNAs (RATEmiRs) database provides a comprehensive catalog of miRNA expression in rat tissues. This resource aids in identifying potential biomarkers for organ damage and disease, facilitating cross-species comparisons with human miRNA data.
Area of Science:
- Genomics and Bioinformatics
- Molecular Biology
- Biomarker Discovery
Background:
- MicroRNAs (miRNAs) are key regulators of gene expression, implicated in various diseases.
- miRNAs show potential as biomarkers for tissue injury and organ damage.
- A comprehensive resource for tissue-specific miRNA expression in rats is needed.
Purpose of the Study:
- To construct a tissue atlas of miRNA abundance in Sprague-Dawley rats.
- To identify tissue-enriched (TE), tissue-specific (TS), and organ-specific (OS) miRNAs.
- To provide a tool for comparing miRNA expression between rat and human tissues.
Main Methods:
- Cataloging miRNA sequencing data from 21 male and 23 female rat tissues.
- Developing algorithms to identify TE, TS, and OS miRNAs by comparative analysis.
- Establishing the Rat Atlas of Tissue-specific and Enriched miRNAs (RATEmiRs) database.
Main Results:
- The RATEmiRs database contains extensive miRNA sequencing data across multiple rat tissues.
- Identification of numerous miRNAs exhibiting tissue-enriched, tissue-specific, or organ-specific expression patterns.
- A functional database is now available for querying miRNA expression profiles.
Conclusions:
- RATEmiRs serves as a valuable resource for researchers studying miRNA function and disease.
- The database facilitates the discovery of novel miRNA biomarkers for organ damage.
- Enables comparative analysis of miRNA expression between rat models and human studies.
