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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...

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...

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Related Experiment Video

Updated: Jun 8, 2026

mirMachine: A One-Stop Shop for Plant miRNA Annotation

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

Target-align: a tool for plant microRNA target identification.

Fuliang Xie¹, Baohong Zhang

¹Department of Biology, East Carolina University, Greenville, NC 27858, USA.

Bioinformatics (Oxford, England)

|October 12, 2010

Summary

We developed Target-align, a new tool for accurately predicting microRNA (miRNA) targets in plants. This method improves upon existing tools by offering greater sensitivity and accuracy for identifying miRNA target sites.

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Last Updated: Jun 8, 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

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Published on: May 25, 2015

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

Published on: January 21, 2020

Area of Science:

Plant biology
Molecular biology
Bioinformatics

Background:

MicroRNAs (miRNAs) are key regulatory molecules in plants.
Identifying miRNA targets is crucial for understanding their function.
Existing tools for plant miRNA target prediction lack reliability.

Purpose of the Study:

To develop a reliable and accurate tool for predicting miRNA targets in plants.
To improve the identification of both cleaved and non-cleaved miRNA target sites.

Main Methods:

Developed a Smith-Waterman-like alignment tool utilizing dynamic programming.
Constructed a score matrix based on nucleotide complementarity for optimal local alignments.
Incorporated parameters like maximum mismatches and consecutive mismatches for filtering alignments.

Main Results:

Target-align demonstrates strong sensitivity and accuracy in predicting miRNA targets compared to other tools.
The tool can identify multi-target sites and potential non-cleaved target sites by adjusting settings.
Available in Windows, web, and command-line versions for diverse user needs.

Conclusions:

Target-align provides a robust solution for plant miRNA target prediction.
The tool's flexibility and accuracy enhance the study of miRNA functions in plants.