Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

scDeepAPA: a deep learning framework for single-cell alternative polyadenylation identification.

Briefings in bioinformatics·2026

Same author

VIRSE: a variational Bayesian framework for RNA structural ensemble inference.

Briefings in bioinformatics·2026

Same author

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

Nature communications·2026

Same author

ShapeRNA: an integrated web server for RNA secondary structure, ensemble, and functional analysis.

Nucleic acids research·2026

Same author

A lncRNA drives developmentally timed decay of all members of an essential microRNA family.

Genes & development·2026

Same author

<i>NRMLncR</i>, a myocyte-enriched long non-coding RNA, enhances myogenesis in mouse.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: Sep 11, 2025

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

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

Lu Li, Peike Sheng, Nicholas M Hiers

Biorxiv : the Preprint Server for Biology

|August 13, 2025

Summary

CLASHub integrates direct miRNA-target interaction data from CLASH experiments with expression data across species. This platform enables discovery of novel microRNA (miRNA) targets and turnover mechanisms, including a new trigger for miR-335-3p degradation.

More Related Videos

Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs

Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs

Published on: June 12, 2018

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: Sep 11, 2025

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

Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs

Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs

Published on: June 12, 2018

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

Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

MicroRNAs (miRNAs) are key regulators of gene expression, crucial in development and disease.
Current methods for identifying miRNA targets, like AGO-CLIP, provide indirect evidence.
CLASH (Crosslinking, Ligation, and Sequencing of Hybrids) offers direct miRNA-target interaction data but has limited datasets.

Purpose of the Study:

To create CLASHub, an integrated online platform for miRNA research.
To combine CLASH data with gene and miRNA expression profiles across multiple species and cell types.
To provide tools for analyzing miRNA interactions and turnover mechanisms, including Target RNA-Directed miRNA Degradation (TDMD).

Main Methods:

Integration of existing CLASH datasets with gene and miRNA expression data from human, mouse, Drosophila, and C. elegans.
Inclusion of datasets with ZSWIM8-knockout to study miRNA turnover.
Development of a user-friendly Analyzer for CLASH, RNA-seq, miRNA-seq, and cumulative fraction curve analysis.

Main Results:

CLASHub provides a comprehensive resource integrating diverse miRNA interaction and expression data.
Analysis using CLASHub revealed a novel TDMD trigger for miR-335-3p degradation within the 3' UTR of ATP6V1G1.
The platform facilitates insights into miRNA turnover mechanisms and target identification.

Conclusions:

CLASHub is a valuable online resource for advancing miRNA research.
The platform enables the discovery of novel miRNA targets and regulatory mechanisms.
It offers powerful analytical tools for exploring miRNA function across various biological contexts.