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Related Concept Videos

Histone Modification02:32

Histone Modification

13.7K
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...
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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...
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Nucleosome Remodeling02:54

Nucleosome Remodeling

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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
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Chromatin Modification in iPS Cells01:32

Chromatin Modification in iPS Cells

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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...
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The Nucleosome Core Particle01:12

The Nucleosome Core Particle

1.2K
Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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Related Experiment Video

Updated: Sep 7, 2025

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis
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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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Investigating Histone Modification Dynamics by Mechanistic Computational Modeling.

Govind Menon1, Martin Howard2

  • 1Department of Computational and Systems Biology, John Innes Centre, Norwich, UK.

Methods in Molecular Biology (Clifton, N.J.)
|June 22, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces a mathematical modeling framework to understand epigenetic memory. It combines computational models with experimental data to explore histone modification dynamics and gene regulation.

Keywords:
BistabilityGene expression statesGillespie algorithmMaintenance and switchingMechanistic modelingNucleosome-mediated epigenetic memoryPolycombStochastic histone modification model

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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:

  • Epigenetics and Molecular Biology
  • Computational Biology and Bioinformatics
  • Systems Biology

Background:

  • Epigenetic memory, crucial for cellular identity, relies on histone modifications.
  • Genome-wide analyses alone are insufficient to elucidate the mechanisms of epigenetic state maintenance and switching.
  • Understanding these dynamics at individual genomic loci requires mechanistic insights.

Purpose of the Study:

  • To present a generic stochastic modeling framework for analyzing histone modification dynamics.
  • To demonstrate the application of this framework using Polycomb-mediated transcriptional silencing.
  • To provide a guide for constructing, simulating, and analyzing such models.

Main Methods:

  • Development of a stochastic modeling framework for histone modification dynamics.
  • Integration of mathematical models with quantitative experimental data (ChIP, mRNA levels, single-cell tracking).
  • Simulation and analysis of a specific case: H3K27 methylation by Polycomb.

Main Results:

  • The proposed framework captures histone modification dynamics, including transcription and feedback loops.
  • The model successfully simulates transcriptional silencing mediated by Polycomb.
  • The approach enables predictions for targeted experimental validation.

Conclusions:

  • Stochastic modeling offers a powerful approach to dissecting epigenetic memory mechanisms.
  • Combining modeling with quantitative data provides deeper mechanistic understanding than purely experimental or computational methods.
  • This framework facilitates the study of complex molecular processes at individual genomic loci.