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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...

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Updated: Apr 26, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

A guide for miRNA target prediction and analysis using web-based applications.

Ana Lúcia Leitão¹, Marina C Costa, Francisco J Enguita

¹Departamento de Ciências e Tecnologia da Biomassa, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus da Caparica, Caparica, 2829-516, Portugal.

Methods in Molecular Biology (Clifton, N.J.)

|July 25, 2014

Summary

MicroRNAs (miRNAs) regulate gene expression by binding to messenger RNA (mRNA). This guide explains practical use of miRNA target prediction algorithms and visualizing results for biological insights.

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Last Updated: Apr 26, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

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Published on: May 1, 2021

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Published on: May 25, 2015

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

Area of Science:

Biochemistry
Molecular Biology
Bioinformatics

Background:

MicroRNAs (miRNAs) are small noncoding RNAs regulating gene expression post-transcriptionally.
miRNA function relies on base complementarity between the miRNA seed sequence and target mRNA 3'UTRs.
Predicting miRNA-target interactions is crucial for understanding gene regulation.

Purpose of the Study:

To provide practical guidance on utilizing miRNA target prediction algorithms.
To demonstrate effective methods for integrating and visualizing prediction results.
To enhance the understanding of miRNA-mediated gene regulation.

Main Methods:

Description of web interfaces for popular miRNA target prediction tools.
Explanation of parameters and considerations for accurate prediction.
Methods for consolidating and graphically presenting prediction data.

Main Results:

Users can effectively employ web-based algorithms for miRNA target prediction.
Integrative approaches allow for clearer visualization of miRNA-binding sites.
Practical strategies enhance the interpretation of miRNA regulatory roles.

Conclusions:

Accessible tools and visualization methods facilitate miRNA target prediction.
Understanding miRNA binding rules is key to accurate functional prediction.
This approach aids in dissecting complex gene regulatory networks.