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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: Apr 10, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.

Krzysztof H Banecki^1,2, Haoxi Chai³, Yijun Ruan³

¹Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland.

Genome Research

|April 8, 2026

Summary

ChromMovie reconstructs 3D chromatin structure by integrating single-cell Hi-C data with cellular trajectories. This novel approach models dynamic changes in chromatin structure throughout processes like the cell cycle.

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Last Updated: Apr 10, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

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Published on: November 3, 2023

High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo

High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo

Published on: August 14, 2020

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:

Genomics
Computational Biology
Molecular Biology

Background:

Three-dimensional (3D) chromatin structure analysis is crucial for understanding genome regulation.
Hi-C and single-cell Hi-C (scHi-C) are key techniques for mapping chromatin interactions.
Existing scHi-C reconstruction methods typically analyze cells individually, limiting insights into dynamic processes.

Purpose of the Study:

To develop a computational framework for reconstructing 3D chromatin structure that incorporates dynamic cellular processes.
To integrate scHi-C contact data with single-cell trajectory information for improved structural modeling.
To bridge the gap between chromatin structure reconstruction and cellular trajectory inference.

Main Methods:

Introduced ChromMovie, a molecular dynamics framework for 3D chromatin structure reconstruction.
Integrated scHi-C contact data with single-cell trajectory information (e.g., cell cycle progression).
Employed simultaneous modeling of multiple cells ordered along a cellular process trajectory.

Main Results:

Successfully recreated known nuclear structures.
Achieved smooth, continuous changes in chromatin structure along cell cycle trajectories.
Demonstrated effective leverage of scHi-C data variability and trajectory information for enhanced reconstruction.

Conclusions:

ChromMovie offers a novel approach to modeling dynamic 3D chromatin structure changes within cellular trajectories.
The framework effectively integrates diverse single-cell data types for more comprehensive genomic analysis.
This work advances the understanding of chromatin dynamics during cellular progression.