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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: May 19, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Quantifying chromatin-associated interactions: the HI-FI system.

Duane D Winkler¹, Karolin Luger, Aaron R Hieb

¹Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.

Methods in Enzymology

|August 23, 2012

Summary

This summary is machine-generated.

This study introduces the HI-FI system, a fluorescence-based method for quantifying interactions between chromatin components and binding factors. It enables high-throughput analysis of chromatin-associated factor function at the molecular level.

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Last Updated: May 19, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

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Published on: May 6, 2010

Capturing Chromosome Conformation Across Length Scales

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Published on: January 20, 2023

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

Area of Science:

Molecular Biology
Biophysics
Genetics

Background:

Chromatin structure is crucial for regulating DNA-based cellular processes.
Interactions with binding factors modulate chromatin and DNA accessibility.
Quantitative in vitro characterization is needed to understand chromatin architecture mechanisms.

Purpose of the Study:

To detail fluorescence methodologies for quantifying thermodynamic principles of chromatin-associated factor interactions.
To introduce the HI-FI (High-throughput Interactions by Fluorescence Intensity) system for this purpose.

Main Methods:

Utilized fluorescence (de)quenching and FRET assays in 384-well microplates.
Employed the HI-FI system for high-throughput, low-concentration interaction characterization.
Developed efficient fluorescent dye attachment protocols for histones and DNA.

Main Results:

The HI-FI system quantifies thermodynamic principles guiding interactions between chromatin components and factors.
Assays are suitable for high-throughput screening and determining complex stoichiometry and interaction sites.
Solution-based assays can be visualized on native gels post-quantification.

Conclusions:

The HI-FI system provides a robust platform for elucidating molecular mechanisms of chromatin-associated factors.
This method offers valuable insights into how factors interact with nucleosomal arrays, mononucleosomes, or components.
Enables detailed mechanistic understanding of chromatin regulation at the molecular level.