Related Experiment Video
Updated: Jun 21, 2026
10:41
An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
Published on: April 5, 2018
Chromatin charting: global mapping of epigenetic effects
1Biotechnology Center for Agriculture and the Environment, Rutgers University, New Brunswick, NJ, USA.
Methods in Molecular Biology (Clifton, N.J.)
|July 10, 2009
Summary
Researchers developed 277 Arabidopsis thaliana lines to study how chromatin organization impacts genome processes like transcription. This resource aids in mapping transgene position effects and epigenetic control for global gene regulation research.
Area of Science:
- Plant molecular biology
- Epigenetics
- Genomics
Background:
- Chromatin organization plays a crucial role in regulating genome-wide processes, including transcription.
- Understanding these organizational principles is key to deciphering gene control mechanisms.
Purpose of the Study:
- To introduce a novel resource for investigating the role of chromatin organization in global gene regulation.
- To enable the study of transgene position effects and epigenetic modifications in response to various cues.
Main Methods:
- Creation of 277 transposon-tagged Arabidopsis thaliana lines.
- Each line contains a single luciferase reporter cassette and a LacO repeat array.
- Visual tracking of tagged regions using fluorescent protein fusion technology.
Main Results:
- The developed resource allows for the mapping of transgene insertion sites and their associated epigenetic states.
- Facilitates the analysis of global epigenetic control in response to developmental and environmental factors.
Conclusions:
- This collection of Arabidopsis lines provides a powerful tool for studying global gene control.
- It opens new avenues for understanding the interplay between chromatin structure and genome regulation in plants.
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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Acetylation
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Acetylation
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Acetylation
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02:25Spreading of Chromatin Modifications
The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
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01:01Euchromatin
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
01:01Euchromatin
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
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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...
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...