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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

Updated: May 9, 2026

CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis
10:40

CRISPR Gene Editing Tool for MicroRNA Cluster Network Analysis

Published on: April 25, 2022

CLASHub is an integrated database and analytical platform for microRNA-target interactions.

Lu Li1,2, Peike Sheng1,2, Nicholas M Hiers1,2,3

  • 1Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA.

Nature Communications
|May 7, 2026
PubMed
Summary
This summary is machine-generated.

CLASHub integrates direct miRNA-target interaction data from CLASH experiments with expression profiles across multiple species and tissues. This platform aids in exploring miRNA regulation and turnover, revealing new targets and degradation mechanisms.

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MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) are key regulators of gene expression, crucial for biological processes and disease states.
  • Current methods for identifying miRNA targets, like AGO-CLIP, provide indirect evidence.
  • CLASH (Crosslinking, Ligation, and Sequencing of Hybrids) offers direct evidence of miRNA-target interactions within Argonaute (AGO) protein complexes.

Purpose of the Study:

  • To develop CLASHub, a comprehensive online platform integrating direct miRNA-target interactions with expression data.
  • To expand the available CLASH datasets across multiple species (human, mouse, Drosophila, C. elegans) and cell types.
  • To provide tools for analyzing miRNA-target interactions and miRNA degradation pathways, including the role of ZSWIM8 in target-directed miRNA degradation (TDMD).

Main Methods:

  • Generation of 91 new CLASH datasets from 17 cell types/tissues across four species.
  • Integration of CLASH data with miRNA and messenger RNA sequencing (RNA-seq) expression data.
  • Development of a user-friendly Analyzer interface for data exploration and analysis, including TDMD pathway analysis.

Main Results:

  • CLASHub provides a unified resource for exploring miRNA-target interactions across diverse biological contexts.
  • Analysis using CLASHub identified a TDMD trigger in the ATP6V1G1 3' UTR for miR-335-3p degradation.
  • Multiple novel targets for miR-18a-5p were discovered through the CLASHub platform.

Conclusions:

  • CLASHub significantly enhances the study of miRNA-target interactions by providing direct, experimentally validated data.
  • The platform facilitates cell/tissue-specific exploration of miRNA regulatory networks and turnover mechanisms.
  • CLASHub is a valuable resource for advancing research in miRNA biology and RNA regulation.