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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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Related Experiment Video

Updated: May 14, 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

Searching the coding region for microRNA targets.

Ray M Marín¹, Miroslav Sulc, Jirí Vanícek

¹École Polytechnique Fédérale de Lausanne,CH-1015 Lausanne, Switzerland.

RNA (New York, N.Y.)

|February 14, 2013

Summary

We developed PACCMIT-CDS, a new algorithm to identify microRNA targets within coding DNA sequences. This method improves accuracy by analyzing conserved, complementary motifs and outperforms existing tools for microRNA target prediction.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Identifying microRNA targets in coding sequences is challenging due to complex amino acid encoding.
Existing algorithms primarily focus on 3' untranslated regions (UTRs).

Purpose of the Study:

To introduce PACCMIT-CDS, a novel algorithm for microRNA target prediction within coding sequences.
To enhance the accuracy and reduce false positives in microRNA target identification.

Main Methods:

Developed PACCMIT-CDS algorithm to search for conserved, seed-complementary motifs in coding sequences.
Utilized a background model that preserves codon usage and amino acid sequence.
Evaluated algorithm performance using Protein-AarLiP (PAR-CLIP) and proteomics data.

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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

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Published on: September 28, 2011

Related Experiment Videos

Last Updated: May 14, 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

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

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Published on: September 28, 2011

Main Results:

PACCMIT-CDS effectively identifies potential microRNA targets within coding sequences.
The algorithm demonstrates a lower false positive rate compared to existing methods.
Achieved superior ranking of predicted microRNA targets.

Conclusions:

PACCMIT-CDS offers a more precise approach to microRNA target prediction in coding regions.
The method provides a valuable tool for understanding microRNA function in gene regulation.