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MicroRNAs

MicroRNAs

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 ends...

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Updated: Jul 1, 2026

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

Published on: April 6, 2012

mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments.

Tzu-Hsien Yang^1,2, Xiang-Wei Li³, Yuan-Han Lee³

¹Department of Biomedical Engineering, National Cheng Kung University, No.1, University Road, Tainan 701, Taiwan.

Database : the Journal of Biological Databases and Curation

|April 5, 2025

Summary

This summary is machine-generated.

Researchers developed mirTarCLASH, a database for exploring microRNA (miRNA) target interactions using chimeric reads from CLASH-like experiments. This platform enhances understanding of miRNA functions by providing user-friendly tools and confidence filters for miRNA-target binding sites.

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Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

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Published on: April 6, 2012

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Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

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Published on: December 1, 2023

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

MicroRNAs (miRNAs) regulate gene expression by targeting messenger RNAs (mRNAs).
Identifying miRNA-target interactions and binding sites is crucial for understanding miRNA functions.
Existing methods like cross-linking, ligation, and sequencing of hybrids (CLASH-seq) generate chimeric reads for direct miRNA-target analysis, but lack accessible platforms.

Purpose of the Study:

To develop a user-friendly database, mirTarCLASH, for efficient exploration of miRNA-target interactions and binding sites.
To provide a comprehensive repository of chimeric reads from CLASH-like experiments in humans, mice, and worms.
To enhance the confidence and visualization of miRNA-binding site data.

Main Methods:

Developed mirTarCLASH, a database integrating 502,061/322,707/224,452 unique hybrid reads from human/mouse/worm miRNA experiments.
Employed the ChiRA algorithm for chimera analysis and RNAup/miRanda tools for binding site inference.
Implemented confidence evaluation filters, including read depth, algorithm support, and cross-linking-induced mutations, with integrated transcript atlas visualization.

Main Results:

The mirTarCLASH database offers a large-scale collection of miRNA-target interactions derived from CLASH-like experiments.
Confidence filters and visualization tools allow for refined analysis and enhanced understanding of miRNA-binding sites.
Demonstrated the database's utility through the well-characterized cel-let-7-5p and lin-41 interaction in C. elegans.

Conclusions:

mirTarCLASH provides a valuable, accessible resource for researchers studying miRNA functions.
The database facilitates the discovery of novel miRNA-target interactions and binding sites.
mirTarCLASH supports subsequent experimental research designs by offering robust data and analytical tools.