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

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Chromatin Immunoprecipitation- ChIP

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

HIV-1 infection converts CD4<sup>+</sup> T cells to HLA class II-restricted CD8<sup>+</sup> T cells.

Science translational medicine·2026

Same author

AF9-KLF2 gene regulatory circuit links histone lactylation to metabolic reprogramming and breast cancer progression.

Cell reports·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

Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.

Genome research·2026

Same journal

EC-isHCR: A rapid method for in situ hybridization chain reaction in diverse animal samples.

Methods (San Diego, Calif.)·2026

Same journal

Single-Molecule methods to investigate mechanisms of transcription by RNA polymerase of Mycobacterium tuberculosis.

Methods (San Diego, Calif.)·2026

Same journal

Detection and sequencing of Usutu virus during mosquito surveillance: Use of multiple assays and techniques for identification at low levels.

Methods (San Diego, Calif.)·2026

Same journal

Experimental validation of an AI-driven digital healthcare platform for oral health behavior and plaque assessment among vietnamese children.

Methods (San Diego, Calif.)·2026

Same journal

Zeta potential: An efficient and cost-effective alternative for investigating cell-surface interactions.

Methods (San Diego, Calif.)·2026

Same journal

An automated workflow for quantifying the formation of synuclein aggregates in human dopaminergic neurons.

Methods (San Diego, Calif.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jan 5, 2026

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

Methods for comparative ChIA-PET and Hi-C data analysis.

Dan Capurso¹, Zhonghui Tang¹, Yijun Ruan²

¹The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.

Methods (San Diego, Calif.)

|October 20, 2019

Summary

This summary is machine-generated.

This review covers methods for analyzing and visualizing chromatin interaction data from ChIA-PET (chromatin interaction analysis with paired-end tag sequencing) and Hi-C (genome-wide chromosome conformation capture) experiments.

More Related Videos

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

Published on: April 11, 2014

Related Experiment Videos

Last Updated: Jan 5, 2026

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

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

Published on: April 11, 2014

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

The 3D chromatin architecture is crucial for genome regulation and function.
High-throughput sequencing methods like ChIA-PET and Hi-C capture chromatin interactions.

Purpose of the Study:

To review methods for comparative analysis and visualization of ChIA-PET and Hi-C data.
To provide guidance on utilizing and interpreting these complex genomic datasets.

Main Methods:

Data acquisition from ENCODE and 4DN portals.
Processing ChIA-PET data with ChIA-PIPE.
Processing Hi-C data using Juicer, distiller, and cooler.
Visualization of 2D contact maps with Juicebox and Higlass.
Analysis of peaks, loops, and domains using BASIC Browser.
Annotation of CTCF loops.

Main Results:

Comprehensive overview of available tools and pipelines for ChIA-PET and Hi-C data.
Detailed steps for data processing, analysis, and visualization.
Methods for identifying and annotating key genomic features like loops and domains.

Conclusions:

Effective analysis and visualization of chromatin interaction data are essential for understanding genome regulation.
This review consolidates current methodologies, facilitating broader adoption and interpretation of ChIA-PET and Hi-C data.