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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...

Heterochromatin

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...

Euchromatin

Euchromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...

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Related Experiment Video

Updated: Jan 12, 2026

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

DiffHiChIP: Identifying differential chromatin contacts from HiChIP data.

Sourya Bhattacharyya¹, Daniela Salgado Figueroa², Katia Georgopoulos³

¹La Jolla Institute for Immunology, La Jolla, CA 92037, USA.

Cell Reports Methods

|November 4, 2025

Summary

This summary is machine-generated.

DiffHiChIP is a new framework for identifying condition-specific loops in chromosome conformation capture (3C) data. It accurately detects differential interactions, including long-range ones, using advanced statistical methods.

Keywords:

3D genome organization CP: computational biology CP: genetics HiChIP chromatin looping differential analysis differential loops

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Related Experiment Videos

Last Updated: Jan 12, 2026

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Chromosome conformation capture (3C) assays like HiChIP are vital for studying interactions between cis-regulatory and structural elements in the genome.
Existing methods for detecting condition-specific loops in 3C data are limited, hindering comprehensive analysis.

Purpose of the Study:

To introduce DiffHiChIP, a novel and comprehensive computational framework for identifying differential loops from HiChIP and similar 3C-based protocols.
To provide a robust statistical approach for detecting condition-specific chromatin interactions.

Main Methods:

DiffHiChIP supports DESeq2 and edgeR, utilizing complete or subset contact maps for background estimation.
It incorporates edgeR with generalized linear models (GLM), offering quasi-likelihood F-test or likelihood ratio test options.
Independent hypothesis weighting (IHW) and distance stratification are implemented to model distance decay and enhance statistical significance.

Main Results:

Analysis of five datasets demonstrates that edgeR GLM-based models with IHW correction effectively identify differential interactions.
The framework accurately captures both short- and long-range differential interactions.
Results are validated against published Hi-C data and reference studies, confirming reliability.

Conclusions:

DiffHiChIP provides a reliable and comprehensive solution for calling differential loops from HiChIP and related 3C assays.
The framework's ability to detect condition-specific interactions, including long-range ones, will be valuable for chromatin regulation studies.
DiffHiChIP is poised to significantly impact the analysis of chromatin conformation data as HiChIP usage grows.