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

RNA-seq

RNA-seq

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...

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

You might also read

Related Articles

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

Sort by

Same author

Pediatric Brain Tumor Consortium phase 1 study of CD40 agonist sotigalimab in pediatric and young adult patients with recurrent CNS tumors and newly-diagnosed DIPG.

Clinical cancer research : an official journal of the American Association for Cancer Research·2026

Same author

Correcting spatial transcriptomics data affected by a prevalent transcript leakage problem across platforms, species, and tissues.

bioRxiv : the preprint server for biology·2026

Same author

A Coral-Inspired Dual Modal Hydrogel Sensor with Deep Learning-Assisted Decoupling of Force-Thermal Stimuli.

ACS applied materials & interfaces·2026

Same author

Multimodal PCSC Sensors for Real-Time Temperature and Force Detection Using LRTNet.

Sensors (Basel, Switzerland)·2026

Same author

Engineering Endogenous T Cell Receptors to Recognize Cancer Neoantigens Using a Hybrid Physics-AI Approach.

bioRxiv : the preprint server for biology·2026

Same author

A Novel Patient-Derived Xenograft Model of Inflammatory Breast Cancer.

Research square·2026

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 24, 2025

Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation

Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation

Published on: April 30, 2012

Proximity Ligation-Assisted ChIP-Seq (PLAC-Seq).

Miao Yu^1,2, Ivan Juric³, Armen Abnousi³

¹Ludwig Institute for Cancer Research, La Jolla, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|August 12, 2021

Summary

This summary is machine-generated.

Proximity ligation-assisted ChIP-Seq (PLAC-Seq), or HiChIP, identifies chromatin contacts linked to specific genomic regions. This method efficiently maps long-range interactions with reduced sequencing costs.

Keywords:

3D genome Chromatin immunoprecipitation Hi-C Long-range chromatin interaction PLAC-Seq

More Related Videos

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

Published on: February 26, 2015

Related Experiment Videos

Last Updated: Oct 24, 2025

Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation

Chromatin Interaction Analysis with Paired-End Tag Sequencing ChIA-PET for Mapping Chromatin Interactions and Understanding Transcription Regulation

Published on: April 30, 2012

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq

Published on: February 26, 2015

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Understanding 3D genome organization is crucial for gene regulation.
Existing methods for chromatin interaction analysis can be costly and complex.
Targeted approaches are needed to study specific genomic loci.

Purpose of the Study:

To introduce and validate Proximity Ligation-assisted ChIP-Seq (PLAC-Seq), also known as HiChIP.
To demonstrate PLAC-Seq's capability in detecting and quantifying specific chromatin contacts.
To highlight the method's efficiency in targeted chromatin organization analysis.

Main Methods:

Combining in situ Hi-C with chromatin immunoprecipitation (ChIP).
Utilizing antibodies against specific transcription factors or histone modifications.
Analyzing targeted genomic regions for chromatin interactions.

Main Results:

PLAC-Seq successfully identifies chromatin contacts anchored at specific genomic regions.
The method achieves kilobase-scale resolution for long-range chromatin interactions.
Significant reduction in sequencing cost compared to other methods.

Conclusions:

PLAC-Seq (HiChIP) is an effective method for targeted chromatin interaction analysis.
It provides high-resolution insights into 3D genome organization at specific loci.
The method offers a cost-effective solution for studying chromatin contacts.