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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: Oct 23, 2025

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

Profiling single-cell chromatin accessibility in plants.

Alexandre P Marand¹, Xuan Zhang¹, Julie Nelson²

¹Department of Genetics, University of Georgia, Athens, GA 30602, USA.

|August 25, 2021

Summary

We present a new protocol for single-cell ATAC-seq in maize, enabling detailed analysis of chromatin accessibility in individual plant cells. This method is adaptable for various plant tissues, revealing cellular variation.

Keywords:

developmental biology genomics molecular biology plant sciences sequence analysis sequencing single cell

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Last Updated: Oct 23, 2025

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

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Published on: February 1, 2022

Area of Science:

Plant genomics
Epigenetics
Molecular biology

Background:

Investigating chromatin accessibility at a single-cell level is crucial for understanding cellular heterogeneity.
Transposase-accessible chromatin sequencing (ATAC-seq) coupled with microfluidics and cellular barcoding offers a powerful approach for this analysis.

Purpose of the Study:

To define a robust protocol for constructing single-cell ATAC-seq libraries from maize seedling nuclei.
To outline preliminary computational steps for assessing the quality of single-cell ATAC-seq data in plants.

Main Methods:

Development of a microfluidic-based protocol for single-cell ATAC-seq library preparation.
Application of cellular barcoding for distinguishing individual cell origins.
Isolation of nuclei from maize seedlings for chromatin accessibility profiling.

Main Results:

Successful construction of single-cell ATAC-seq libraries from maize seedling nuclei.
Establishment of preliminary computational pipelines for data quality assessment.

Conclusions:

The developed protocol provides a valuable tool for studying chromatin accessibility variation at the single-cell level in maize.
This method is adaptable to other plant species and tissues, facilitating broader applications in plant epigenomics.