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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...

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Updated: Jun 6, 2026

Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs

Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs

Published on: June 12, 2018

miRTarBase: a database curates experimentally validated microRNA-target interactions.

Sheng-Da Hsu¹, Feng-Mao Lin, Wei-Yun Wu

¹Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan.

Nucleic Acids Research

|November 13, 2010

Summary

The miRTarBase database curates experimentally validated microRNA-target interactions (MTIs). This resource aids in understanding miRNA functions and developing computational tools for MTI identification.

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Area of Science:

Genetics
Molecular Biology
Bioinformatics

Background:

MicroRNAs (miRNAs) are small non-coding RNAs regulating protein expression.
Accurate miRNA-target interaction (MTI) data is crucial for understanding cellular mechanisms.
Existing databases lack comprehensive, experimentally validated MTI collections.

Purpose of the Study:

To establish a comprehensive, manually curated database of experimentally validated miRNA-target interactions (MTIs).
To provide a reliable resource for researchers studying miRNA functions across different species.
To supply positive samples for developing computational methods for MTI prediction.

Main Methods:

Systematic literature mining and text data mining to identify relevant research articles.
Manual curation of miRNA-target interactions from selected studies.
Experimental validation of MTIs using reporter assays, western blots, or microarrays.

Main Results:

The miRTarBase database contains 3576 experimentally verified MTIs.
These interactions involve 657 miRNAs and 2297 target genes across 17 species.
miRTarBase offers the largest collection of validated MTIs compared to other databases.

Conclusions:

miRTarBase is a valuable, continuously updated resource for miRNA research.
The database facilitates the elucidation of miRNA functions and regulatory networks.
It serves as a critical resource for advancing computational MTI identification methods.