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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 27, 2025

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

Design and Construction of a Focused DNA-Encoded Library for Multivalent Chromatin Reader Proteins.

Justin M Rectenwald¹, Shiva Krishna Reddy Guduru², Zhao Dang²

¹UNC School of Medicine, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Molecules (Basel, Switzerland)

|February 27, 2020

Summary

Researchers developed a DNA-Encoded Library (DEL) of 60,000 compounds to discover inhibitors for chromatin reader domains, crucial for understanding epigenetics and treating diseases.

Keywords:

DNA-Encoded Libraries chromatin reader protein target-class drug discovery

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Last Updated: Dec 27, 2025

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

Adaptation of Hybridization Capture of Chromatin-associated Proteins for Proteomics to Mammalian Cells

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Published on: June 1, 2018

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Area of Science:

Epigenetics and Molecular Biology
Chemical Biology
Drug Discovery

Background:

Chromatin structure and function are regulated by histone post-translational modifications (PTMs).
Chromatin reader proteins recognize these PTMs, influencing cellular phenotype and gene regulation.
Dysregulation of chromatin pathways is linked to various human diseases, highlighting the need for therapeutic interventions.

Purpose of the Study:

To design and construct a focused DNA-Encoded Library (DEL) targeting bi-valent methyl-lysine (Kme) reader domains.
To develop chemical probes for inhibiting chromatin reader functions and advance understanding of chromatin dynamics.
To establish a rapid discovery method for inhibitors of multivalent chromatin reader domains.

Main Methods:

Utilized computational methods and structure-based knowledge for library design.
Synthesized a focused DEL comprising approximately 60,000 compounds.
Developed DNA-barcoded control compounds for optimizing selection conditions.

Main Results:

Successfully designed and constructed a targeted DEL for bi-valent methyl-lysine reader domains.
Established a method for optimizing selection conditions using model Kme reader domains.
Demonstrated a focused approach for discovering chromatin reader inhibitors.

Conclusions:

The developed DEL provides a valuable tool for targeting Kme reader domains.
This approach facilitates the rapid discovery of inhibitors for multivalent chromatin reader proteins.
The findings offer new avenues for therapeutic strategies targeting epigenetic misregulation.