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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: Feb 27, 2026

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

NicE-seq: high resolution open chromatin profiling.

V K Chaithanya Ponnaluri¹, Guoqiang Zhang¹, Pierre-Olivier Estève¹

¹New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA.

|June 29, 2017

Summary

This summary is machine-generated.

NicE-seq offers high-resolution open chromatin profiling for both native and fixed cells. This new method reveals transcription factor occupancy and active regulatory elements with single-nucleotide precision.

Keywords:

DNA methylation NicE-seq Open chromatin Transcription factor occupancy

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Last Updated: Feb 27, 2026

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Published on: December 12, 2017

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

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Published on: October 14, 2022

Area of Science:

Genomics
Epigenetics
Molecular Biology

Background:

Open chromatin profiling identifies transcriptionally active genomic regions.
Existing methods like DNase-seq and ATAC-seq often require native cells or large cell quantities.
A need exists for methods applicable to both native and fixed cells with high resolution.

Purpose of the Study:

To introduce NicE-seq (nicking enzyme assisted sequencing), a novel method for open chromatin profiling.
To demonstrate NicE-seq's capability for high-resolution analysis on both native and formaldehyde-fixed cells.
To characterize open chromatin sites (OCSs) and transcription factor occupancy using NicE-seq.

Main Methods:

NicE-seq utilizes nicking enzymes to identify open chromatin regions.
The method achieves single-nucleotide resolution for OCSs and transcription factor occupancy.
NicE-seq was applied to both native and formaldehyde-fixed cells.

Main Results:

NicE-seq successfully identified open chromatin sites (OCSs) with high resolution.
Results from NicE-seq were coincident with DNase hypersensitive sites and ATAC-seq sites, requiring lower sequencing depth.
OCSs identified by NicE-seq correlated with RNA polymerase II occupancy and active chromatin marks.
A contrasting pattern was observed between OCSs and CpG methylation.
Decitabine treatment leading to hypomethylation in HCT116 cells resulted in an increased number of OCSs.

Conclusions:

NicE-seq provides a versatile and high-resolution method for open chromatin profiling.
The technique is effective on both native and fixed cells, broadening its applicability.
NicE-seq offers valuable insights into genome regulation, transcription factor binding, and epigenetic modifications.