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Nucleosome Remodeling

Nucleosome Remodeling

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...

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,...

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...

Inheritance of Chromatin Structures

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...

Duplication of Chromatin Structure

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...

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.
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Related Experiment Video

Updated: Jul 12, 2026

Generation and Purification of Human INO80 Chromatin Remodeling Complexes and Subcomplexes

Generation and Purification of Human INO80 Chromatin Remodeling Complexes and Subcomplexes

Published on: October 23, 2014

Models for chromatin remodeling: a critical comparison.

K van Holde¹, T Yager

¹Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA.

Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire

|August 5, 2003

Summary

Nucleosome remodeling involves DNA movement, differing from random diffusion. A twist-defect model explains ATP-dependent remodeling, addressing recent challenges and proposing a resolution to model discrepancies.

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Generation and Purification of Human INO80 Chromatin Remodeling Complexes and Subcomplexes

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Area of Science:

Molecular Biology
Biophysics
Chromatin Dynamics

Background:

Nucleosome remodeling often involves cis displacement of nucleosomes along DNA.
This process is unidirectional and ATP-dependent, distinguishing it from random nucleosome diffusion.
Existing models, like the twist-defect diffusion model, explain some remodeling observations.

Purpose of the Study:

To address recent experimental findings that challenge the twist-defect diffusion model for nucleosome remodeling.
To discuss the apparent favorability of the reptation model over the twist-defect model.
To propose a resolution reconciling discrepancies between theoretical models and experimental data in nucleosome remodeling.

Main Methods:

Review and analysis of existing theoretical models for nucleosome migration and remodeling.
Comparison of model predictions with recent experimental data on nucleosome dynamics.
Development of a modified model to incorporate ATP-dependent defect generation and address discrepancies.

Main Results:

The twist-defect diffusion model, while successful in explaining some aspects, faces challenges from recent experimental studies.
Experimental data appear to support a reptation model for nucleosome remodeling.
The study identifies specific problems with the current twist-defect model's applicability.

Conclusions:

Reconciling the twist-defect and reptation models is crucial for a comprehensive understanding of ATP-dependent nucleosome remodeling.
A proposed resolution aims to bridge the gap between theoretical frameworks and empirical evidence.
Further research is needed to fully elucidate the mechanisms of nucleosome dynamics and remodeling.