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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.
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Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
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Chromatin Modification in iPS Cells01:32

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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.
Compact chromatin makes reprogramming difficult. Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. Molecules that inhibit histone...
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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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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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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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Combinatorial Gene Control02:33

Combinatorial Gene Control

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Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Related Experiment Video

Updated: Aug 28, 2025

Oct4GiP Reporter Assay to Study Genes that Regulate Mouse Embryonic Stem Cell Maintenance and Self-renewal
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Oct4GiP Reporter Assay to Study Genes that Regulate Mouse Embryonic Stem Cell Maintenance and Self-renewal

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OCT4 interprets and enhances nucleosome flexibility.

Caitlin M MacCarthy1, Jan Huertas1,2, Claudia Ortmeier1

  • 1Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany.

Nucleic Acids Research
|September 21, 2022
PubMed
Summary
This summary is machine-generated.

Pioneer transcription factors like Oct4 open chromatin by interacting with nucleosomes. Their DNA binding domains stabilize flexible, open nucleosome structures, influencing cellular identity.

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Area of Science:

  • Molecular Biology
  • Chromatin Dynamics
  • Epigenetics

Background:

  • Pioneer transcription factors (PTFs) are crucial for cellular reprogramming, initiating changes in cell identity by accessing condensed chromatin.
  • PTFs bind to inaccessible DNA regions, promoting chromatin opening and recruiting other regulatory factors.
  • The precise mechanisms by which PTFs interact with nucleosomes, the fundamental units of chromatin, remain incompletely understood, particularly regarding structural dynamics.

Purpose of the Study:

  • To elucidate the structural basis of how the pioneer transcription factor Oct4 interacts with and modulates nucleosome structural flexibility.
  • To investigate the role of Oct4's DNA binding domains in stabilizing open nucleosome conformations.
  • To understand how nucleosome dynamics are influenced by Oct4 binding site position and histone tail mobility.

Main Methods:

  • Utilized a combination of experimental techniques and molecular dynamics simulations.
  • Investigated the interaction between the Oct4 protein and nucleosomes.
  • Analyzed the impact of Oct4 binding on nucleosome structural flexibility and dynamics.

Main Results:

  • Oct4 binding significantly enhances nucleosome structural flexibility.
  • The extent of Oct4's influence on nucleosome dynamics is dependent on the specific DNA binding site location and the mobility of histone tails.
  • Oct4 employs both specific DNA sequence recognition and non-specific DNA interactions via its two DNA binding domains to stabilize open nucleosome structures.

Conclusions:

  • Oct4 actively remodels nucleosomes, promoting structural flexibility and open conformations essential for its function as a master regulator of pluripotency.
  • The findings provide a detailed structural perspective on how pioneer factors engage with nucleosomes, highlighting the adaptability of transcription factors in chromatin modulation.
  • This work offers insights into the dynamic interplay between transcription factors and chromatin, crucial for understanding cellular identity transitions and epigenetic regulation.