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Related Concept Videos

Histone Modification02:32

Histone Modification

14.9K
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...
14.9K
Histone Modification02:32

Histone Modification

3.9K
3.9K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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...
8.8K
Histone Variants at the Centromere02:30

Histone Variants at the Centromere

4.6K
Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
4.6K

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Updated: Nov 4, 2025

Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF
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Author Spotlight: Enhanced Histone PTM Isomer Identification Through LC-TIMS-ToF MS/MS and PASEF

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PTMViz: a tool for analyzing and visualizing histone post translational modification data.

Kevin Chappell1, Stefan Graw1,2, Charity L Washam1,2

  • 1Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St. slot 516, Little Rock, AR, 72205, USA.

BMC Bioinformatics
|May 27, 2021
PubMed
Summary
This summary is machine-generated.

PTMViz analyzes histone post-translational modifications (PTMs) and protein abundance from mass spectrometry data. This tool helps identify epigenetic changes and differentially expressed proteins, aiding disease research.

Keywords:
Differential abundanceHistone post-translational modificationsProteomicsShiny

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Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue
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Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Genomics

Background:

  • Histone post-translational modifications (PTMs) regulate chromatin structure and gene expression.
  • Aberrant histone PTMs are linked to diseases like cancer.
  • Mass spectrometry generates large datasets requiring advanced bioinformatics for analysis.

Purpose of the Study:

  • To develop PTMViz, a bioinformatics tool for differential abundance analysis and visualization of protein and histone PTMs.
  • To facilitate the exploration of mass spectrometry data for identifying regulatory changes.

Main Methods:

  • PTMViz utilizes the Shiny platform for interactive data tables and visualization plots.
  • The tool enables comparison of protein and histone PTMs between two sample groups.
  • Differential abundance analysis is performed on mass spectrometry-derived data.

Main Results:

  • PTMViz presents significantly differentiated proteins and histone PTMs.
  • Interactive visualizations allow users to distinguish between protein abundance and epigenetic changes.
  • Analysis of methamphetamine-treated mice revealed differentially regulated proteins and histone PTMs (H3K9me, H3K27me3, H4K16ac).

Conclusions:

  • Histone modifications are crucial for gene expression regulation.
  • PTMViz offers an interactive platform for rapid identification of differentially expressed proteins and PTMs from mass spectrometry data.