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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...

Spreading of Chromatin Modifications

Spreading of Chromatin Modifications

The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...

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Related Experiment Video

Updated: Sep 25, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

Chromatin accessibility profiling by ATAC-seq.

Fiorella C Grandi^1,2,3, Hailey Modi^1,2,3, Lucas Kampman^1,2,3

¹Gladstone Institute of Neurological Disease, San Francisco, CA, USA.

Nature Protocols

|April 28, 2022

Summary

This summary is machine-generated.

This study presents Omni-ATAC, an optimized protocol for assay for transposase-accessible chromatin using sequencing (ATAC-seq). Omni-ATAC efficiently maps the chromatin landscape across diverse cell types for disease and perturbation studies.

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Last Updated: Sep 25, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

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Area of Science:

Molecular Biology
Genomics
Epigenetics

Background:

Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is a scalable method to profile chromatin accessibility.
Understanding chromatin landscape alterations is crucial for studying cell type-specific changes in disease or response to perturbations.
Existing ATAC-seq protocols may require optimization for broad applicability.

Purpose of the Study:

To describe an updated and optimized protocol for ATAC-seq, named Omni-ATAC.
To provide a protocol applicable across a wide range of cell and tissue types.
To detail steps for generating and sequencing ATAC-seq libraries and recommendations for analysis.

Main Methods:

The Omni-ATAC protocol involves five key steps: sample preparation, transposition, library preparation, sequencing, and data analysis.
The protocol is designed for scalability and requires a relatively small number of input cells.
It does not necessitate prior knowledge of specific epigenetic marks or transcription factors.

Main Results:

Omni-ATAC is applicable to diverse cell and tissue types.
ATAC-seq libraries for approximately 12 samples can be generated within 10 hours by individuals with basic molecular biology skills.
Downstream sequencing analysis can be performed using established pipelines with access to high-performance computing.

Conclusions:

Omni-ATAC offers an efficient and versatile method for chromatin accessibility profiling.
The protocol facilitates the study of chromatin dynamics in various biological contexts, including disease and perturbation.
Omni-ATAC streamlines the generation and analysis of ATAC-seq data, making it accessible to researchers with standard molecular biology and bioinformatics expertise.