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

CRISPR and crRNAs

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...

You might also read

Related Articles

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

Sort by

Same author

[Characteristics of the Pathogenic Bacteria Isolated from the Lower Respiratory Tract of the Patients With Acute Exacerbation of Chronic Obstructive Pulmonary Disease].

Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition·2026

Same author

[Microbiological Characteristics of Extrapulmonary Nontuberculous Mycobacterial Infections in a Tertiary Hospital].

Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition·2026

Same author

Automated SPE-GC-MS/MS method for the biomonitoring of eight <i>N</i>-nitrosamines in human urine.

Analytical methods : advancing methods and applications·2026

Same author

Erratum: IGF2BP2-modified UBE2D1 Interacts with Smad2/3 to Promote the Progression of Breast Cancer.

American journal of cancer research·2026

Same author

scMVAF: a multi-view adaptive fusion clustering approach for single-cell RNA-sequencing data.

Briefings in bioinformatics·2026

Same author

Molecular analysis of polymyxin B resistance in clinical carbapenem-resistant Klebsiella pneumoniae isolates from a large tertiary care teaching hospital in Southwest China.

BMC microbiology·2026

Search research articles

Related Experiment Video

Updated: Sep 21, 2025

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

circRIP: an accurate tool for identifying circRNA-RBP interactions.

Xin Dong¹, Ke Chen², Wenbo Chen¹

¹School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China.

Briefings in Bioinformatics

|May 31, 2022

Summary

This summary is machine-generated.

Researchers developed circRIP, an efficient algorithm to identify genome-wide interactions between circular RNAs (circRNAs) and RNA-binding proteins (RBPs). This tool enhances understanding of circRNA functions by analyzing RIP-Seq and eCLIP data.

Keywords:

RIP-Seq RNA-binding protein circRNA eCLIP

More Related Videos

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

Related Experiment Videos

Last Updated: Sep 21, 2025

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Published on: October 21, 2022

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC

Published on: May 9, 2020

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Published on: April 30, 2011

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

Circular RNAs (circRNAs) are key regulators of gene expression, primarily through interactions with RNA-binding proteins (RBPs).
Identifying circRNA-RBP interactions genome-wide is crucial for understanding circRNA function, but efficient computational tools are lacking.

Purpose of the Study:

To develop and validate an efficient algorithm, circRIP, for identifying circRNA-RBP interactions from RIP-Seq and eCLIP data.
To demonstrate the utility of circRIP in discovering circRNA-RBP interactions in specific biological contexts.

Main Methods:

Development of the circRIP algorithm for analyzing RIP-Seq and eCLIP datasets to predict circRNA-RBP interactions.
Simulation testing to evaluate the sensitivity and specificity of the circRIP algorithm.
Application of circRIP to identify circRNAs bound by IGF2BP3 and to survey circRNA-RBP interactions in K562 and HepG2 cell lines.

Main Results:

The circRIP algorithm demonstrated high sensitivity and specificity in simulation tests.
Identification of 95 IGF2BP3-binding circRNAs using IGF2BP3 RIP-Seq data.
Discovery of 2823 and 1333 circRNAs interacting with over 100 RBPs in K562 and HepG2 cell lines, respectively, using eCLIP data.

Conclusions:

circRIP is an accurate and sensitive tool for systematically identifying RBP and circRNA interactions.
The tool facilitates genome-wide surveys of circRNA-RBP interactions, significantly aiding functional exploration of circRNAs.
This work provides a valuable resource for researchers investigating the roles of circRNAs and their protein interactions.