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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 Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
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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 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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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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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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Related Experiment Video

Updated: Jan 7, 2026

Biochemical Assays for Analyzing Activities of ATP-dependent Chromatin Remodeling Enzymes
10:14

Biochemical Assays for Analyzing Activities of ATP-dependent Chromatin Remodeling Enzymes

Published on: October 25, 2014

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Rotational settings quantize nucleosome movement by chromatin regulators.

Van La1, Abby Trouth1, Vijay Ramani2,3

  • 1Structural Biology, Biochemistry, and Biophysics Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.

Biorxiv : the Preprint Server for Biology
|December 25, 2025
PubMed
Summary

DNA sequence intrinsically guides nucleosome positioning across species, challenging current models. Chromatin regulators navigate these DNA-encoded preferences, not override them, in a

Keywords:
10 bp quantized shiftsRotational positioninghigh-resolution mapping

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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
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Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Proper nucleosome positioning is crucial for gene regulation and genomic integrity.
  • Existing models suggest chromatin regulators override intrinsic DNA sequence preferences for nucleosome placement.
  • The precise role of DNA sequence in guiding nucleosome structure in vivo remains debated.

Purpose of the Study:

  • To investigate the intrinsic role of DNA sequence in guiding nucleosome structure and remodeling.
  • To determine if DNA sequence preferences are conserved across species.
  • To propose a new model for nucleosome positioning.

Main Methods:

  • In vitro nucleosome reconstitution assays.
  • Analysis of nucleosome positioning in yeast and mammalian cells.
  • Heterologous insertion of foreign DNA sequences into the yeast genome.
  • Investigating the influence of chromatin remodelers and transcription elongation.

Main Results:

  • DNA sequences intrinsically guide nucleosome structure and remodeling from yeast to mammals.
  • Nucleosomes exhibit preferences for specific dinucleotide arrangements (A/T inward, G/C outward) at ~10 bp intervals.
  • Heterologously inserted DNA sequences in yeast also follow these intrinsic positioning rules.
  • Chromatin remodelers and transcription elongation modulate, but do not override, these DNA sequence-based preferences.

Conclusions:

  • DNA sequence actively dictates preferred rotational settings for nucleosomes every ~10 bp.
  • Chromatin regulators operate within the energy landscape established by DNA sequence.
  • The 'quantized ratchet' model unifies understanding of precise nucleosome positioning by integrating DNA sequence and regulatory factors.