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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...

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...

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: Jun 22, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH.

Chikako Ragan¹, Nicole Cloonan, Sean M Grimmond

¹The University of Queensland, Institute for Molecular Bioscience, and ARC Centre of Excellence in Bioinformatics, Brisbane, Australia.

|May 30, 2009

Summary

We developed FASTH, a computational tool to predict microRNA (miRNA) target sites by analyzing RNA structure. This method reveals numerous favorable binding sites across the transcriptome, impacting gene regulation across species and transcript variants.

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Last Updated: Jun 22, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

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Published on: May 1, 2021

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

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

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

MicroRNAs (miRNAs) regulate gene expression through base-pairing with messenger RNAs (mRNAs).
Predicting miRNA target sites is complex due to secondary structures and varying binding affinities.

Purpose of the Study:

To develop an efficient computational method for genome-scale prediction of miRNA target sites.
To analyze miRNA-mRNA interactions across human and mouse transcriptomes using a thermodynamic approach.

Main Methods:

Introduction of FASTH software for predicting miRNA target sites based on minimizing free energy of duplex structure.
Application of the approach to human and mouse transcriptomes.
Validation of predicted miRNA-mRNA interactions using luciferase assays.

Main Results:

Identification of abundant, energetically favorable miRNA binding sites beyond validated targets, occurring across all mRNA regions.
Prediction of significant differences in target sites among transcript isoforms and between human and mouse orthologs.
Experimental validation of four out of six predicted miRNA-mRNA interactions, showing an average 73% reduction in mRNA levels.

Conclusions:

A thermodynamically based computational approach can be scaled for transcriptome-wide miRNA target site prediction.
miRNA regulation is species- and transcript-specific, with implications for diverse biological contexts.
FASTH provides a robust tool for understanding miRNA-mediated gene regulation.