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Related Concept Videos

Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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 DNA...
Histone Modification02:32

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 Modification02:32

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,...
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

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...
Heterochromatin02:38

Heterochromatin

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 9th...
Heterochromatin02:38

Heterochromatin

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 9th...

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Chromatin Extraction from Frozen Chimeric Liver Tissue for Chromatin Immunoprecipitation Analysis
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Published on: March 23, 2021

Chromatin computation: epigenetic inheritance as a pattern reconstruction problem.

Christian Arnold1, Peter F Stadler, Sonja J Prohaska

  • 1Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany; Harvard University, Department of Human Evolutionary Biology, 11 Divinity Avenue, Cambridge, MA 02138, USA.

Journal of Theoretical Biology
|July 25, 2013
PubMed
Summary
This summary is machine-generated.

Cellular epigenetic memory relies on reconstructing histone modifications after replication. Our simulations show enzymes can maintain chromatin states, but success depends on various factors influencing error accumulation.

Keywords:
Chromatin complexityChromatin computationEpigenetic inheritanceEvolutionary algorithmGillespie algorithmHistone modifications

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A Method to Study de novo Formation of Chromatin Domains
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A Method to Study de novo Formation of Chromatin Domains
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A Method to Study de novo Formation of Chromatin Domains

Published on: August 23, 2019

Area of Science:

  • Epigenetics and chromatin biology
  • Computational biology and systems biology
  • Molecular and cellular biology

Background:

  • Eukaryotic histones undergo diverse chemical modifications crucial for cellular state and transcriptional regulation.
  • DNA replication disrupts chromatin states, leading to partial erasure of epigenetic information.
  • Mechanisms for reconstructing histone modifications post-replication are poorly understood.

Purpose of the Study:

  • To test the hypothesis that histone-modifying enzymes can recompute parental histone modification patterns using partial information.
  • To develop a computational model for simulating the dynamics of histone modification states during cell division.

Main Methods:

  • Developed a stochastic simulation system based on Gillespie's approach to model detailed chemical dynamics.
  • Utilized an evolutionary algorithm to accurately find patterns across multiple cell divisions.
  • Simulated enzyme systems to assess their ability to maintain chromatin states.

Main Results:

  • Evolved enzyme systems can maintain chromatin states stably, even without distinct domain boundaries.
  • System stability is sensitive to initial state length, target pattern, replication timing, and enzyme kinetics.
  • These factors also impact the accumulation of errors across cell divisions.

Conclusions:

  • A theoretical mechanism for maintaining epigenetic memory via histone modification recomputation is feasible.
  • Enzyme-mediated chromatin state maintenance is possible but influenced by unanticipated factors.
  • Understanding these factors is critical for comprehending epigenetic inheritance and error propagation.