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Related Concept Videos

Histone Modification02:32

Histone Modification

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,...
Histone Modification02:32

Histone Modification

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,...
Euchromatin01:01

Euchromatin

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...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...
Spreading of Chromatin Modifications02:25

Spreading 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.
Writers
The writer is an enzyme that can...

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Related Experiment Video

Updated: Jun 21, 2026

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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

High throughput characterization of combinatorial histone codes.

Nicolas L Young1, Peter A DiMaggio, Mariana D Plazas-Mayorca

  • 1Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA.

Molecular & Cellular Proteomics : MCP
|August 6, 2009
PubMed
Summary

We developed a new "saltless" chromatography method coupled with mass spectrometry to rapidly analyze complex histone modifications. This technique significantly reduces sample needs and analysis time for high-throughput histone code characterization.

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Analysis of Histone Antibody Specificity with Peptide Microarrays
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Analysis of Histone Antibody Specificity with Peptide Microarrays

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Related Experiment Videos

Last Updated: Jun 21, 2026

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin
24:02

The ChroP Approach Combines ChIP and Mass Spectrometry to Dissect Locus-specific Proteomic Landscapes of Chromatin

Published on: April 11, 2014

Analysis of Histone Antibody Specificity with Peptide Microarrays
09:47

Analysis of Histone Antibody Specificity with Peptide Microarrays

Published on: August 1, 2017

Area of Science:

  • Proteomics
  • Chromatography
  • Mass Spectrometry

Background:

  • Histone modifications form the "histone code" regulating gene expression.
  • Characterizing complex combinatorial histone codes is challenging due to sample requirements and analytical limitations.

Purpose of the Study:

  • To develop a novel, automated, high-throughput method for characterizing hypermodified combinatorial histone codes.
  • To improve upon existing methods by reducing sample requirements and analysis time.

Main Methods:

  • Utilized "saltless" pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC).
  • Directly coupled WCX-HILIC to electron transfer dissociation (ETD) mass spectrometry (MS).
  • Employed a benchtop linear quadrupole ion trap MS for analysis of eluted histone peptides.

Main Results:

  • Achieved a 100-fold reduction in sample requirements and analysis time compared to existing methods.
  • Identified all major combinatorial histone codes within a 2-hour analysis.
  • Successfully resolved and distinguished isobaric modifications (e.g., trimethyl and acetyl) using combined MS and chromatographic data.
  • Characterized over 200 H3.2 and 70 H4 forms, including novel, highly modified variants.

Conclusions:

  • The developed "saltless" WCX-HILIC-ETD-MS method provides efficient and sensitive characterization of histone codes.
  • This technique enables the detailed analysis of complex histone modifications, crucial for understanding epigenetic regulation.
  • The methodology is broadly applicable to highly modified peptides and isomeric species separation.