Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

RNA-seq03:21

RNA-seq

10.1K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.1K

You might also read

Related Articles

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

Sort by
Same author

Classification and Quantification of Unproductive Splicing Events.

Acta naturae·2025
Same author

Post-transcriptional Regulation of Gene Expression via Unproductive Splicing.

Acta naturae·2024
Same author

Cooperation and Competition of RNA Secondary Structure and RNA-Protein Interactions in the Regulation of Alternative Splicing.

Acta naturae·2024
Same author

Tandem Exon Duplications Expanding the Alternative Splicing Repertoire.

Acta naturae·2022
Same author

Neuronal metabolism governs cortical network response state.

Proceedings of the National Academy of Sciences of the United States of America·2006
Same author

[Assessment of nutrition in dialysis patients and chronic uremic patients].

Zhonghua nei ke za zhi·1999

Related Experiment Video

Updated: Jul 31, 2025

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

12.1K

RNAcontacts: A Pipeline for Predicting Contacts from RNA Proximity Ligation Assays.

S D Margasyuk1, M A Vlasenok1, G Li2

  • 1Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation.

Acta Naturae
|May 8, 2023
PubMed
Summary

We developed RNAcontacts, a new pipeline for analyzing RNA-RNA contacts in living cells using proximity ligation assays. This method improves the detection sensitivity and specificity of RNA interactions, aiding in spatial transcriptomics research.

Keywords:
RNARNA contactsRNA structureproximity ligationsplicing

More Related Videos

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
07:24

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

2.5K
A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

11.8K

Related Experiment Videos

Last Updated: Jul 31, 2025

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
11:32

Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen

Published on: May 24, 2017

12.1K
Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
07:24

Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA

Published on: July 9, 2021

2.5K
A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
13:00

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA

Published on: December 2, 2009

11.8K

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • High-throughput RNA proximity ligation assays enable simultaneous analysis of RNA spatial proximity in cells.
  • These methods involve cross-linking, fragmentation, and religation of RNAs, followed by sequencing.
  • A key challenge is mapping sequencing fragments with two distinct split types: pre-mRNA splicing and RNA ligation.

Purpose of the Study:

  • To present RNAcontacts, a universal bioinformatics pipeline for detecting RNA-RNA contacts from proximity ligation assays.
  • To address the challenge of mapping complex sequencing data with dual split types.
  • To provide a sensitive and specific method for identifying RNA-RNA interactions.

Main Methods:

  • Developed RNAcontacts, a two-pass alignment pipeline.
  • The first pass infers splice junctions from control RNA-seq data.
  • The second pass uses inferred splice junctions as bona fide introns for alignment.

Main Results:

  • RNAcontacts achieves more sensitive detection of RNA contacts compared to existing methods.
  • The pipeline demonstrates higher specificity in identifying bona fide splice junctions.
  • RNAcontacts automates contact extraction, clustering, read support computation, and visualization track generation.

Conclusions:

  • RNAcontacts is a versatile pipeline for RNA-RNA contact detection applicable to various proximity ligation methods.
  • The pipeline enhances the analysis of spatial RNA interactions.
  • RNAcontacts is implemented in Snakemake for reproducible and scalable data processing and is publicly available.