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Related Concept Videos

Histone Modification02:32

Histone Modification

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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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The Nucleosome Core Particle01:12

The Nucleosome Core Particle

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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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The Nucleosome Core Particle02:10

The Nucleosome Core Particle

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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.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
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Heterochromatin02:38

Heterochromatin

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

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Combinatorial Histone Acetylation Patterns Are Generated by Motif-Specific Reactions.

Thomas Blasi1, Christian Feller2, Justin Feigelman1

  • 1Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Chair of Mathematical Modeling of Biological Systems, Technische Universität München, Center for Mathematics, 85748 Garching, Germany.

Cell Systems
|May 3, 2016
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Summary

Histone acetylation patterns are formed by specific pathways, not random processes. Our computational model reveals motif-specific acetylation activity drives these complex patterns in Drosophila melanogaster.

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Purification of H3 and H4 Histone Proteins and the Quantification of Acetylated Histone Marks in Cells and Brain Tissue
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Area of Science:

  • Biochemistry and Molecular Biology
  • Genomics and Epigenetics
  • Computational Biology

Background:

  • Post-translational modifications (PTMs) like histone acetylation regulate gene expression and cellular functions.
  • Understanding the combinatorial patterns (motifs) of PTMs is crucial but challenging.
  • Previous models of acetylation lacked the specificity to explain observed patterns.

Purpose of the Study:

  • To develop a computational framework for analyzing histone acetylation patterns.
  • To investigate the design principles governing combinatorial acetylation on histone H4 in Drosophila melanogaster.
  • To identify specific acetylation pathways responsible for generating observed PTM motifs.

Main Methods:

  • Development of an open-source computational framework.
  • Modeling acetylation rates based on site-specific and motif-specific activities.
  • Comparison of model predictions with experimentally determined motif abundances.
  • Validation of predicted acetylation pathways using enzyme depletion data.

Main Results:

  • Models with unspecific or lysine site-specific acetylation rates failed to explain motif abundances.
  • An ensemble of models with motif-specific acetylation rates best described the data.
  • Four distinct acetylation pathways were identified by the model ensemble.
  • Three of the four predicted pathways were validated through experimental data.

Conclusions:

  • Histone acetylation patterns are generated by specific, rather than random, mechanisms.
  • Motif-specific acetylation activity is a key determinant of combinatorial PTM patterns.
  • The developed computational framework provides insights into epigenetic regulation.
  • Specific acetylation pathways underlie the formation of histone acetylation motifs.