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Related Concept Videos

MicroRNAs01:22

MicroRNAs

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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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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...
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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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RIMap-RISC: a transcriptome-wide database of structurally modeled human microRNA interactions.

Simon Chasles1,2, Zakary Gaillard-Duchassin1,2, Jordan Quenneville1

  • 1Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, QC, H3C 3J7, Canada.

Genome Biology
|February 26, 2026
PubMed
Summary
This summary is machine-generated.

RIMap-RISC is a new database for modeling human microRNA (miRNA) targeting. It predicts and details miRNA-transcript interactions using a biophysical framework, offering a novel approach to understanding gene regulation.

Keywords:
Computational RNA biologyDissociation constantsMicroRNA targetingNon-canonical interactionsPost-transcriptional regulationRNA accessibilityRNA duplex structureRNA regulonsTranscriptome-wide analysis

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • MicroRNA (miRNA) targeting is crucial for gene regulation.
  • Existing tools lack comprehensive biophysical modeling of miRNA-target interactions.
  • Understanding miRNA binding sites requires considering secondary structures and energetics.

Purpose of the Study:

  • To develop a web-accessible database for transcriptome-wide modeling of human miRNA targeting.
  • To provide detailed information on predicted miRNA-transcript interactions.
  • To introduce a novel framework integrating biophysical principles and secondary structure prediction.

Main Methods:

  • Development of the RIMap-RISC database and its web interface.
  • Implementation of a biophysical model for miRNA-RISC complex interactions.
  • Integration of duplex secondary structure prediction, free energy calculations, and site classification.
  • Incorporation of target accessibility and evolutionary conservation analysis.

Main Results:

  • RIMap-RISC computes and records transcript-miRNA interaction details including position, structure, energy, and conservation.
  • The database supports transcript-wide queries via an interactive interface and RESTful API.
  • A novel miRNA-centric nomenclature for interaction types is introduced.
  • The model accommodates seed and supplementary pairing within a bipartite RISC architecture.

Conclusions:

  • RIMap-RISC offers a comprehensive platform for exploring miRNA targeting.
  • The integrated biophysical framework provides deeper insights into miRNA-RNA interactions.
  • The database facilitates research in gene regulation and miRNA function.