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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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Updated: Feb 21, 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

Second-generation method for analysis of chromatin binding with formaldehyde-cross-linking kinetics.

Hussain Zaidi¹, Elizabeth A Hoffman², Savera J Shetty²

¹From the School of Medicine Research Computing, University of Virginia and.

The Journal of Biological Chemistry

|October 4, 2017

Summary

Formaldehyde cross-linking kinetics (CLK) assays were refined using budding yeast to better measure protein-DNA interactions. Optimized conditions improve accuracy for in vivo binding kinetics on the minute timescale.

Keywords:

chromatin immunoprecipitation (ChiP)chromatin structure formaldehyde chemistry nucleic acid chemistry protein cross-linking protein dynamic transcription factor

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Last Updated: Feb 21, 2026

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

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Published on: April 2, 2018

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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:

Molecular Biology
Biochemistry
Genetics

Background:

Formaldehyde cross-linking is crucial for studying protein-DNA interactions in chromatin.
Existing methods for assessing binding kinetics are challenging and require high precision.
Understanding formaldehyde's behavior in vivo is essential for accurate data interpretation.

Purpose of the Study:

To biochemically characterize formaldehyde cross-linking properties in budding yeast.
To improve the cross-linking kinetics (CLK) assay for measuring in vivo binding kinetics.
To provide a more precise method for analyzing chromatin-protein interactions.

Main Methods:

Utilized time-dependent formaldehyde cross-linking experiments in budding yeast.
Optimized formaldehyde concentration and glycine-quench conditions for the CLK assay.
Analyzed the kinetics of various protein-DNA interactions in vivo.

Main Results:

Formaldehyde cross-linking rates vary significantly between different protein-DNA interactions.
Some interactions cross-link rapidly, enabling kinetic analysis.
Other interactions cross-link slowly, allowing equilibrium binding constant determination but not on/off rates.

Conclusions:

The study provides a refined CLK assay for accurate in vivo binding kinetics on the minute timescale.
Optimized formaldehyde cross-linking conditions enhance the reliability of chromatin interaction studies.
This work advances the understanding of formaldehyde's role in chromatin research and kinetic analysis.