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Related Concept Videos

Histone Modification02:32

Histone Modification

18.0K
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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Histone Modification02:32

Histone Modification

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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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Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
The basic unit of the chromatin is the nucleosome, consisting of DNA wrapped around octameric histone proteins and short stretches of linker DNA separating individual nucleosomes. The histone proteins within the nucleosome have their...
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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: Apr 20, 2026

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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Mechanistic stochastic model of histone modification pattern formation.

Lisette C M Anink-Groenen1, Timo R Maarleveld2, Pernette J Verschure1

  • 1Swammerdam Institute for Life Science (SILS), University of Amsterdam, Science Park 904, P.O. Box 94215, 1098 GE Amsterdam, The Netherlands.

Epigenetics & Chromatin
|November 20, 2014
PubMed
Summary

Histone modification patterns form dynamically on genes through enzyme diffusion and recruitment. Chromatin connectivity creates stable, bistable states crucial for gene expression regulation.

Keywords:
Bistable dynamicsBoundary formationChromatin structureCooperative interactionsEpigeneticsHistone modification patternsStochastic mathematical 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:

  • Molecular Biology
  • Systems Biology
  • Epigenetics

Background:

  • Gene activity is regulated by chromatin structure, including nucleosome dynamics and histone modifications.
  • The precise mechanisms and temporal dynamics of histone modification patterns remain poorly understood.

Purpose of the Study:

  • To develop a stochastic mathematical model for histone modification pattern formation on single genes.
  • To investigate the roles of enzyme diffusion, recruitment, and chromatin connectivity in pattern dynamics.

Main Methods:

  • Developed a stochastic mathematical model with non-phenomenological, physical parameters.
  • Simulated histone modification pattern formation dynamics on a single gene model.

Main Results:

  • Diffusion and recruitment of histone-modifying enzymes, along with chromatin connectivity, drive diverse stochastic dynamics.
  • Rapid pattern establishment/removal occurs via diffusion and weak recruitment; strong synergism creates stable, irreversible patterns.
  • Chromatin connectivity induces bistability, enabling state switching and forming stable, long-range or localized patterns regulating gene expression.

Conclusions:

  • Cooperative interactions between regulatory proteins and chromatin state generate complex stochastic gene expression dynamics.
  • The model provides physical insights into the formation and stability of epigenetic patterns.