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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...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Related Experiment Video

Updated: Jun 7, 2026

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

miRBase: integrating microRNA annotation and deep-sequencing data.

Ana Kozomara¹, Sam Griffiths-Jones

¹Faculty of Life Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.

Nucleic Acids Research

|November 2, 2010

Summary

This summary is machine-generated.

miRBase is a comprehensive database for microRNA sequences and annotations, now including deep-sequencing data. This resource aids in discovering novel microRNAs and understanding their expression patterns across tissues and stages.

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A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

miRBase is the leading online repository for microRNA (miRNA) sequences and annotations.
The latest release (miRBase 16) encompasses over 15,000 miRNA gene loci across 140+ species and 17,000+ distinct mature miRNA sequences.
Advancements in deep-sequencing technologies have accelerated the discovery of novel miRNAs.

Purpose of the Study:

To integrate and present deep-sequencing data within the miRBase repository.
To develop user-friendly web interfaces for exploring miRNA deep-sequencing mappings.
To provide tools for analyzing miRNA expression and annotation evidence.

Main Methods:

Mapping short RNA deep-sequencing reads to existing miRBase miRNA annotations.
Developing web interfaces for data visualization and analysis.
Implementing search functionalities for tissue- and stage-specific miRNA expression.

Main Results:

Successful mapping of deep-sequencing reads to miRBase annotations.
Creation of web tools enabling users to view read data, filter by experiment and count, and search for specific miRNA expression profiles.
Demonstration of how deep-sequencing data can serve as a proxy for relative miRNA expression levels.

Conclusions:

The integrated deep-sequencing data enhances the utility of miRBase for miRNA research.
The developed web interfaces facilitate detailed examination of miRNA annotations and isoforms.
This resource supports the validation of existing annotations and the identification of novel miRNA insights.