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Updated: Jun 26, 2026

Detection of Histone Modifications in Plant Leaves

Detection of Histone Modifications in Plant Leaves

Published on: September 23, 2011

A simple, robust, cost-effective, and low-input ChIP-seq method for profiling histone modifications and Pol II in

Danling Zhu¹, Yi Wen¹, Yifang Tan¹

¹Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Research, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.

The New Phytologist

|September 15, 2024

Summary

We developed Ultrasensitive Plant ChIP-seq (UP-ChIP), a cost-effective method for epigenetic studies. UP-ChIP requires minimal plant material and labor, making it ideal for sensitive profiling of histone modifications and Pol II.

Keywords:

ChIP‐seq Pol II epigenetics histone modifications seeds

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Last Updated: Jun 26, 2026

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Published on: April 22, 2022

Area of Science:

Plant epigenetics
Molecular genetics
Chromatin biology

Background:

Chromatin immunoprecipitation and sequencing (ChIP-seq) is crucial for epigenetic studies but is costly and requires substantial plant material.
Conventional ChIP-seq faces challenges with fatty acid-rich samples like seeds.
Existing methods are labor-intensive and resource-demanding.

Purpose of the Study:

To develop a highly sensitive and cost-effective ChIP-seq method for plants.
To enable epigenetic profiling with reduced sample input and labor.
To provide a reliable alternative to traditional ChIP-seq for various plant tissues.

Main Methods:

Developed Ultrasensitive Plant ChIP-seq (UP-ChIP) using native ChIP coupled with Tn5 tagmentation.
Applied UP-ChIP to profile histone modifications and RNA Polymerase II (Pol II).
Validated UP-ChIP across diverse plant samples, including seedlings, seeds, and sorted nuclei.

Main Results:

UP-ChIP significantly reduces antibody and bead requirements per immunoprecipitation (IP).
The method effectively utilizes starting material amounts as low as a few milligrams.
UP-ChIP demonstrates high reliability, sensitivity, and quantitative accuracy for histone modification studies.
Applicable to various plant samples, including challenging seed tissues.

Conclusions:

UP-ChIP offers a less labor-intensive and more cost-effective alternative to traditional ChIP-seq.
The method is suitable for profiling histone modifications and Pol II in diverse plant samples.
UP-ChIP enables epigenetic research with significantly lower sample input requirements.