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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...

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Related Experiment Video

Updated: Dec 26, 2025

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

Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data.

Shounak Chakraborty^1,2,3,4, Stefan Canzar⁴, Tobias Marschall^2,3

¹Cluster of Excellence for Multimodal Computing and Interaction, Saarland University, Saarland Informatics Campus E1.7, Saarbrücken, Germany.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|March 12, 2020

Summary

This study introduces ChromaClique, a new method to analyze cell subpopulation nucleosome profiles from NOMe-seq data. ChromaClique accurately deconvolutes distinct chromatypes, advancing epigenetic gene regulation studies.

Keywords:

HMMs NOMe-seq epigenetics max clique enumeration

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Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

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Last Updated: Dec 26, 2025

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

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

Area of Science:

Genomics
Epigenetics
Computational Biology

Background:

Analyzing nucleosome positioning is vital for understanding epigenetic gene regulation.
Current genome-wide assays often use bulk sequencing, limiting the analysis of individual cell subpopulations.
Reconstructing distinct nucleosome profiles (chromatypes) from heterogeneous cell populations is a significant challenge.

Purpose of the Study:

To develop a novel computational approach for deconvoluting nucleosome profiles from single NOMe-seq measurements.
To enable the analysis of chromatypes within cell subpopulations.
To overcome the limitations of bulk sequencing in studying cellular heterogeneity in nucleosome positioning.

Main Methods:

Utilized the NOMe-seq assay characteristics to create a new deconvolution method called ChromaClique.
Employed a maximal clique enumeration algorithm on a novel NOMe read graph.
Computed graph edge probabilities efficiently using hidden Markov models.

Main Results:

ChromaClique successfully deconvolutes different chromatypes from single NOMe-seq experiments.
The method demonstrates higher accuracy compared to a related existing approach using simulated data.
ChromaClique exhibits favorable scalability for genome-wide analyses.

Conclusions:

ChromaClique provides an accurate and scalable solution for analyzing cell subpopulation nucleosome profiles.
This method enhances the study of epigenetic gene regulation by resolving cellular heterogeneity.
Genome-wide chromatype analysis in cell subpopulations is now feasible with NOMe-seq and ChromaClique.