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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: Aug 5, 2025

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

Determining chromatin architecture with Micro Capture-C.

Joseph C Hamley¹, Hangpeng Li¹, Nicholas Denny¹

¹MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.

Nature Protocols

|March 29, 2023

Summary

This summary is machine-generated.

Micro Capture-C (MCC) is a high-resolution chromatin conformation capture method. It visualizes genome 3D contacts, revealing regulatory elements like transcription factor binding sites.

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Last Updated: Aug 5, 2025

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

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Published on: October 14, 2022

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

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

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Chromatin conformation capture (3C) methods assay genome topology using proximity ligation.
Existing 3C techniques have limitations in resolution and scope.
Visualizing fine-scale chromatin interactions is crucial for understanding gene regulation.

Purpose of the Study:

To introduce Micro Capture-C (MCC) as an advanced 3C method.
To demonstrate MCC's capability for high-resolution genome contact mapping.
To highlight MCC's utility in studying regulatory elements.

Main Methods:

MCC refines 3C techniques for enhanced resolution.
Utilizes a sequence-agnostic nuclease and full sequencing of ligation junctions.
Maintains cellular integrity throughout the process.

Main Results:

Achieves subnucleosomal resolution, surpassing previous 3C methods.
Successfully visualizes challenging loci such as gene-dense regions and super-enhancers.
Identifies transcription factor binding sites with DNAse I footprinting-like resolution.

Conclusions:

MCC provides unprecedented resolution for mapping 3D genome architecture.
Enables detailed analysis of regulatory element interactions.
Offers a powerful tool for genomic research, requiring molecular biology and bioinformatics expertise.