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Histone Modification

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 Modification

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,...

Chromatin Modification in iPS Cells

Chromatin Modification in iPS Cells

Chromatin modification alters gene expression; therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...

Spreading of Chromatin Modifications

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...

Chromatin Structure Regulates pre-mRNA Processing

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...

Epigenetic Regulation

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...

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Related Experiment Video

Updated: May 10, 2026

Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue

Global Level Quantification of Histone Post-Translational Modifications in a 3D Cell Culture Model of Hepatic Tissue

Published on: May 5, 2022

Modeling exon expression using histone modifications.

Shijia Zhu¹, Guohua Wang, Bo Liu

¹Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.

|July 5, 2013

Summary

This summary is machine-generated.

Histone modifications in transcribed regions better predict gene expression than promoter modifications. New models reveal how histone marks regulate exon splicing, offering insights into gene regulation.

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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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Published on: May 5, 2022

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

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Extraction of Histones from Clinical Specimens for Epigenetic Profiling by Mass Spectrometry

Extraction of Histones from Clinical Specimens for Epigenetic Profiling by Mass Spectrometry

Published on: November 21, 2025

Area of Science:

Molecular Biology
Epigenetics
Genomics

Background:

Histone modifications are crucial for gene expression regulation.
Previous research primarily focused on histone modifications at gene promoters.
The impact of histone modifications on transcribed regions and exon splicing remains less understood.

Purpose of the Study:

To investigate the role of histone modifications in transcribed regions of genes.
To develop quantitative models for predicting gene expression and alternative exon expression based on histone modifications.
To explore the interaction network between histone modifications and exon splicing.

Main Methods:

Construction of quantitative models to predict gene expression variation from histone modifications in transcribed regions.
Development of a model to predict alternative exon expression using histone modifications on exons.
Construction of an interaction network using partial correlations to link histone modifications with alternative exon expression.

Main Results:

A quantitative model based on transcribed regions predicted gene expression more accurately than a promoter-based model.
The exon expression model proved general across different exon and cell types.
Specific histone modifications (H3K36me3, H4K20me1) were identified as directly influencing exon expression, with others acting additively.

Conclusions:

Histone modifications within transcribed regions significantly impact gene expression and exon splicing.
Combinations of histone modifications contribute to exon splicing in a redundant and cumulative manner.
This study enhances the understanding of histone modification effects on gene transcription and splicing.