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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: Jan 13, 2026

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation

Profiling of H3K4me3 Modification in Plants using Cleavage under Targets and Tagmentation

Published on: April 22, 2022

Practical NicE-seq workflow for chromatin accessibility analysis in plants.

Zein Eddin Bader¹, Nassem Albakri², Dae-Jin Yun²

¹Reproductive System RIKEN ECL Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.

Molecules and Cells

|January 8, 2026

Summary

This summary is machine-generated.

This study introduces a computational framework for analyzing NicE-seq data in plants, an alternative to ATAC-seq for open chromatin profiling. It guides researchers in using NicE-seq, especially for challenging samples like archived tissues.

Keywords:

ATAC-seq Analysis Chromatin NicE-seq

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Area of Science:

Plant epigenomics
Computational biology
Molecular biology

Background:

Open chromatin profiling reveals regulatory DNA accessible to transcription factors, crucial for gene regulation.
Standard methods like ATAC-seq and DNase-seq have limitations, requiring large cell numbers or fresh samples.
NicE-seq provides an alternative using nicking endonucleases and polymerase-mediated biotin labeling.

Purpose of the Study:

To present a detailed analysis framework for NicE-seq data in plants.
To adapt and modify the nf-core/atacseq pipeline for NicE-seq.
To guide researchers in applying NicE-seq and choosing between NicE-seq and ATAC-seq.

Main Methods:

Developed a computational framework for NicE-seq data analysis in Arabidopsis thaliana.
Adapted the nf-core/atacseq pipeline with specific modifications for NicE-seq.
Detailed data processing, peak calling, annotation, and integration with transcriptomic data.

Main Results:

Established a robust workflow for NicE-seq data analysis in plants.
Highlighted analytical differences between NicE-seq and ATAC-seq.
Demonstrated the utility of NicE-seq for challenging sample types.

Conclusions:

The presented framework facilitates NicE-seq data analysis in plant epigenomic research.
NicE-seq is a valuable tool for studying open chromatin, particularly with limited or archived samples.
This resource aids researchers in selecting appropriate open chromatin profiling techniques.