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

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

You might also read

Related Articles

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

Sort by
Same author

RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.

Nucleic acids research·2026
Same author

Building an Interoperable Rare Disease Multi-omic Resource: The GREGoR Data Model and Dataset.

bioRxiv : the preprint server for biology·2026
Same author

Application of intelligent technologies for dysphagia risk prediction: A scoping review.

Digital health·2026
Same author

Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells.

bioRxiv : the preprint server for biology·2026
Same author

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors.

GigaScience·2026
Same author

Long-read MitoScope reveals tissue-resolved somatic mitochondrial variation and landscape of nuclear-embedded mitochondrial sequences.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Jun 17, 2026

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
21:55

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

Published on: April 30, 2012

Chromatin interaction analysis using paired-end tag sequencing.

Melissa J Fullwood1, Yuyuan Han, Chia-Lin Wei

  • 1Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.

Current Protocols in Molecular Biology
|January 14, 2010
PubMed
Summary
This summary is machine-generated.

Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET) maps genome-wide protein-mediated DNA interactions. This technique reveals higher-order chromatin structures in mammalian cells using next-generation sequencing.

More Related Videos

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
10:41

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo
12:36

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Published on: January 14, 2016

Related Experiment Videos

Last Updated: Jun 17, 2026

Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for Mapping Chromatin Interactions and Understanding Transcription Regulation
21:55

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

Published on: April 30, 2012

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
10:41

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo
12:36

Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo

Published on: January 14, 2016

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Understanding higher-order chromatin structure is crucial for gene regulation.
  • Existing methods have limitations in large-scale, de novo analysis of chromatin interactions.

Purpose of the Study:

  • To describe the Chromatin Interaction Analysis using Paired-End Tag sequencing (ChIA-PET) technique.
  • To provide a method for genome-wide analysis of protein-mediated chromatin interactions in mammalian cells.

Main Methods:

  • Cells are cross-linked with formaldehyde to preserve interactions.
  • Protein-bound DNA is enriched via chromatin immunoprecipitation.
  • Interacting DNA fragments are ligated and sequenced using Paired-End Tag (PET) strategies.
  • Bioinformatics analysis of sequencing data generates interaction maps.

Main Results:

  • ChIA-PET enables large-scale, de novo mapping of chromatin interactions.
  • The technique identifies genome-wide binding sites and interactions mediated by specific protein factors.
  • Application with Roche/454 and Illumina sequencing technologies is demonstrated.

Conclusions:

  • ChIA-PET is a powerful tool for dissecting higher-order chromatin organization.
  • This method facilitates comprehensive analysis of protein-DNA interactions across the genome.
  • The described protocol is applicable to mammalian systems for detailed chromatin structure studies.