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Related Concept Videos

MicroRNAs01:22

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...
MicroRNAs01:22

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...
MicroRNAs01:22

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

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mirMachine: A One-Stop Shop for Plant miRNA Annotation
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Published on: May 1, 2021

MMpred: functional miRNA--mRNA interaction analyses by miRNA expression prediction.

Przemyslaw A Stempor1, Michael Cauchi, Paul Wilson

  • 1Cranfield Health, Cranfield University, Vincent Building, Cranfield, UK. p.stempor@gurdon.cam.ac.uk

BMC Genomics
|November 16, 2012
PubMed
Summary

This study introduces MMpred, a novel pipeline for analyzing microRNA (miRNA)-messenger RNA (mRNA) interactions using only mRNA expression data. MMpred accurately predicts miRNA targets and biological relationships, aiding hypothesis generation.

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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

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • MicroRNA (miRNA)-directed gene repression is a key posttranscriptional regulatory mechanism.
  • Paired miRNA-mRNA expression datasets are scarce, hindering comprehensive analysis.
  • Primary miRNAs are often co-expressed with host genes, suggesting regulatory links.

Purpose of the Study:

  • To develop a computational pipeline for predicting miRNA-mRNA interactions using only mRNA expression data.
  • To overcome the limitation of limited paired miRNA-mRNA expression datasets.
  • To enable functional enrichment analyses of predicted miRNA targets.

Main Methods:

  • Developed the MMpred pipeline utilizing scaling function and linear models for miRNA expression prediction.
  • Employed miRNA-mRNA anti-correlation analysis to identify probable miRNA gene targets.
  • Integrated stringent statistical methods for prediction consistency and accuracy.
  • Performed functional enrichment analyses (GO, KEGG, DO) on predicted targets.

Main Results:

  • MMpred requires only mRNA expression data, independent of third-party miRNA target prediction tools.
  • The pipeline demonstrated accuracy validated by binding energy between mature miRNA and target 3' UTR.
  • MMpred generated results comparable to those from paired miRNA-mRNA datasets.
  • Consistent output and predicted biological relationships were achieved for test cases.

Conclusions:

  • MMpred offers a robust solution for miRNA-mRNA interaction analysis with limited data.
  • The pipeline facilitates the generation of testable hypotheses for further biological investigation.
  • MMpred enhances the understanding of miRNA-mediated gene regulation.