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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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A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

A Reporter Assay to Analyze Intronic microRNA Maturation in Mammalian Cells

Published on: June 16, 2022

MicroRNA promoter analysis.

Molly Megraw¹, Artemis G Hatzigeorgiou

¹Department of Genetics, Center for Bioinformatics, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

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

|October 6, 2009

Summary

This summary is machine-generated.

This chapter guides predicting plant microRNA (miRNA) promoter elements using transcription factor binding motifs. It details a method using Positional Weight Matrices (PWMs) for Arabidopsis transcription factors (TFs).

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Area of Science:

Plant molecular biology
Genomics
Bioinformatics

Background:

Plant microRNAs (miRNAs) regulate gene expression.
Understanding miRNA promoters is crucial for gene regulation studies.
Existing databases lack comprehensive plant miRNA promoter information.

Purpose of the Study:

To provide a practical guide for predicting plant miRNA promoter elements.
To detail a method for identifying transcription factor binding sites (TFBSs) in plant miRNA promoters.
To offer a resource for researchers studying plant gene regulation.

Main Methods:

Overview of current knowledge on plant miRNA promoters.
Step-by-step guide for predicting miRNA promoter elements.
Utilizing a collection of Positional Weight Matrices (PWMs) for Arabidopsis transcription factors (TFs).
Applying TF-specific scoring thresholds for potential binding sites.
Searching for TFBSs in pol-II promoter regions.

Main Results:

A practical approach for predicting plant miRNA promoter elements is presented.
The method allows for the identification of TFBSs in plant miRNA promoters.
The described procedure is particularly useful for plant miRNA promoters.

Conclusions:

The developed method enhances the prediction of plant miRNA promoter elements.
This guide facilitates research into plant gene regulation via miRNAs.
Resources for prediction are available online.