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Chromatin Immunoprecipitation- ChIP

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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.
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Related Experiment Video

Updated: Jun 18, 2025

Chromatin Isolation by RNA Purification ChIRP

Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

Chrom-seq identifies RNAs at chromatin marks.

Ligang Fan^1,2, Wei Sun, Yitong Lyu²

¹Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi'an, China.

Science Advances

|July 31, 2024

Summary

This summary is machine-generated.

We developed Chrom-seq, a new method to identify RNAs associated with chromatin marks in living cells. This technique efficiently maps regulatory RNAs involved in epigenetic events without needing antibodies.

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Area of Science:

Molecular Biology
Epigenetics
Genomics

Background:

Chromatin marks regulate gene transcription, but identifying associated long non-coding RNAs (lncRNAs) is challenging.
Existing methods for RNA-chromatin association detection are limited by antibody requirements and high noise from crosslinking.

Purpose of the Study:

To develop a novel, efficient, and antibody-free method for capturing RNAs directly associated with specific chromatin marks in living cells.
To systematically map lncRNAs involved in epigenetic regulation.

Main Methods:

Developed Chrom-seq, combining specific chromatin mark readers with APEX2 proximity labeling.
RNAs adjacent to chromatin marks were biotinylated and isolated using streptavidin beads.
Utilized readers for H3K27me3, H3K9me3, and H3K4me3 marks.

Main Results:

Chrom-seq successfully detected RNA species associated with H3K27me3, H3K9me3, and H3K4me3.
The method demonstrated superior sensitivity, efficiency, and cost-effectiveness compared to existing techniques.
Identified potential regulatory RNAs at specific epigenetic marks.

Conclusions:

Chrom-seq offers a powerful, antibody-free approach to map chromatin-associated RNAs in living cells.
This method facilitates the systematic study of lncRNAs in epigenetic regulation.
Enables deeper understanding of RNA's role in chromatin organization and function.