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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: Jan 2, 2026

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Published on: August 13, 2020

An optimized protocol for isolating primary epithelial cell chromatin for ChIP.

James A Browne¹, Ann Harris², Shih-Hsing Leir¹

¹Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, Illinois, United States of America; Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America.

|June 28, 2014

Summary

Optimizing chromatin purification is key for robust chromatin immunoprecipitation sequencing (ChIP-seq). This study presents a modified protocol for preparing high-quality ChIP-grade chromatin from primary human epithelial cells, overcoming common lysis challenges.

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Last Updated: Jan 2, 2026

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Published on: August 13, 2020

Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples

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Published on: August 29, 2017

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
Genomics
Cell Biology

Background:

Robust chromatin immunoprecipitation sequencing (ChIP-seq) relies on optimized chromatin purification and size selection.
Standard ENCODE protocols face challenges with primary human epithelial cells due to their tendency to form resistant sheets, hindering lysis and causing sonication contamination.
Effective chromatin isolation is crucial for accurate genome-wide identification of DNA-binding protein targets.

Purpose of the Study:

To develop an optimized protocol for preparing high-quality ChIP-grade chromatin from primary human bronchial epithelial cells.
To address the specific challenges of chromatin isolation and size selection in epithelial cells.
To provide a reproducible method for obtaining sheared chromatin suitable for ChIP applications.

Main Methods:

Modification of the standard ENCODE protocol by incorporating key steps before cell lysis.
Pre-lysis treatment included short incubation in Trypsin-EDTA, equilibration in detergent-free buffers, addition of Triton X-100 to lysis buffer, and needle passage with agitation.
Microscopic visualization using Methyl Green-Pyronin dye was employed to document each step and assess chromatin quality.

Main Results:

The optimized protocol effectively separates formaldehyde-fixed epithelial cell sheets prior to lysis.
High-quality, sheared chromatin suitable for ChIP was reproducibly obtained from primary human bronchial epithelial cells.
Microscopic analysis confirmed the effectiveness of each modification in preparing the chromatin.

Conclusions:

The modified protocol successfully overcomes the challenges of chromatin preparation from primary human epithelial cells.
This method yields high-quality ChIP-grade chromatin, essential for reliable ChIP-sequencing experiments.
The protocol is adaptable for use with other epithelial cell types, broadening its applicability.