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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

11.1K
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...
11.1K

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Related Experiment Video

Updated: Jun 24, 2026

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)
09:52

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)

Published on: April 19, 2013

High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq.

Aanchal Choudhary1, Moonia Ammari1, Hyuk Sung Yoon1

  • 1Waksman Institute of Microbiology, Department of Plant Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.

Nucleic Acids Research
|November 26, 2024
PubMed
Summary

We developed PHILO ChIP-seq, a cost-effective platform for plant transcription factor (TF) binding and chromatin dynamics. This method enables large-scale analysis, revealing new insights into gene regulation in plants.

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Last Updated: Jun 24, 2026

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)
09:52

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)

Published on: April 19, 2013

TChIP-Seq: Cell-Type-Specific Epigenome Profiling
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Published on: January 23, 2019

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies
08:04

A Semiautomated ChIP-Seq Procedure for Large-scale Epigenetic Studies

Published on: August 13, 2020

Area of Science:

  • Plant molecular biology
  • Epigenetics
  • Genomics

Background:

  • Assessing transcription factor (TF) binding and chromatin dynamics in plants at scale is challenging.
  • Existing methods often require substantial starting material and can be costly.
  • Understanding genome-wide TF binding and histone modifications is crucial for plant gene regulation.

Purpose of the Study:

  • To introduce PHILO (Plant HIgh-throughput LOw input) ChIP-seq, a novel high-throughput platform for plant epigenomic studies.
  • To enable cost-effective and extensive capture of TF binding and histone modification distributions.
  • To facilitate complex experimental setups for plant research.

Main Methods:

  • Development of the PHILO ChIP-seq pipeline, adaptable to various plant species.
  • Utilizing low input material (1mg) and optional micrococcal nuclease (MNase) for chromatin fragmentation.
  • Application of H3K9ac PHILO ChIP-seq to analyze eight Arabidopsis thaliana jasmonic acid (JA) pathway mutants, processing over 100 samples.

Main Results:

  • Successfully recapitulated and expanded knowledge of the interplay between master TFs (MYC2/3/4) and chromatin regulators in Arabidopsis.
  • Discovered novel histone acetylation patterns in regulatory regions of MYC2 target genes in Arabidopsis.
  • Demonstrated conservation of these acetylation patterns in tomato (Solanum lycopersicum).

Conclusions:

  • The PHILO ChIP-seq platform is highly effective for large-scale investigation of TF binding and chromatin dynamics in plants.
  • This platform supports cost-efficient complex experimental designs.
  • It opens new avenues for understanding plant epigenomes and gene regulation.