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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: Jan 2, 2026

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells

Published on: April 2, 2018

A method for assessing histone surface accessibility genome-wide.

Luke T Marr¹, David J Clark², Jeffrey J Hayes¹

¹Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.

Methods (San Diego, Calif.)

|December 13, 2019

Summary

This summary is machine-generated.

This study introduces a novel method to assess histone protein surface accessibility in chromatin. This technique aids in understanding genome organization and gene regulation by mapping functional genomic elements.

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Last Updated: Jan 2, 2026

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells

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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

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

DNA is compacted into nucleosomes and higher-order chromatin structures, organizing the genome for essential processes like gene expression and cell division.
Chromatin structure regulates DNA accessibility through histone post-translational modifications and chromatin remodeling factors.
Assessing chromatin accessibility genome-wide is crucial for identifying functional elements like enhancers and promoters.

Purpose of the Study:

To develop and demonstrate a general method for assessing the accessibility of internal and external histone protein surfaces.
To provide a new tool for investigating genome-wide chromatin accessibility.

Main Methods:

Engineered cysteine residues on specific histone protein surfaces in S. cerevisiae.
Assessed histone surface exposure using a thiol-specific reagent, biotin-maleimide.
Purified modified nucleosomes via a one-step process, followed by library preparation and deep sequencing.

Main Results:

The developed method successfully assessed histone protein surface accessibility.
Modified nucleosomes were enriched approximately 25-fold over background signals.
Nucleosome phasing relative to transcription start sites was consistent with unselected populations.

Conclusions:

The described method is feasible for assessing histone surface accessibility in chromatin.
This technique offers a valuable approach for mapping functional genomic elements and understanding gene regulation.
The findings provide insights into the organization and accessibility of the genome within nucleosomes.