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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: Dec 11, 2025

Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease

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Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input.

Tetsuya Handa¹, Akihito Harada², Kazumitsu Maehara²

¹Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Japan.

Nature Protocols

|August 19, 2020

Summary

Chromatin integration labeling followed by sequencing (ChIL-seq) offers a low-input method for epigenomic profiling. This technique amplifies target genomic sequences before cell lysis, enabling sensitive detection of protein and modification localization.

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

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Published on: April 5, 2018

Area of Science:

Molecular Biology
Epigenetics
Genomics

Background:

Cell identity relies on gene regulation via transcription factors and epigenetic modifications.
Chromatin immunoprecipitation (ChIP) is the standard for mapping these genomic events.
Increasing demand for low-input epigenomic profiling necessitates alternative methods.

Purpose of the Study:

To detail the protocol for Chromatin Integration Labeling followed by sequencing (ChIL-seq).
To provide assessment methods for key ChIL-seq steps.
To make ChIL-seq more accessible for precious and single-cell samples.

Main Methods:

ChIL-seq utilizes an oligonucleotide-conjugated antibody (ChIL probe) for in situ labeling.
Target genomic sequences are amplified via Tn5 transposase and T7 RNA polymerase.
The protocol includes steps for ChIL probe reaction, transposition, in situ transcription, and library preparation.

Main Results:

ChIL-seq enables detection of antibody target localization at both the microscopic and genomic levels.
The protocol is optimized for low-input samples, including single cells.
Detailed assessment methods for critical steps are provided.

Conclusions:

ChIL-seq is a powerful, accessible technique for epigenomic profiling of limited samples.
The described protocol facilitates wider adoption and further applications of ChIL-seq.
The method supports multitarget analysis for comprehensive epigenomic studies.