Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

The Nucleosome Core Particle01:12

The Nucleosome Core Particle

902
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...
902
The Nucleosome01:19

The Nucleosome

1.4K
Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
1.4K
Histone Modification02:32

Histone Modification

13.2K
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...
13.2K
Nucleosome Remodeling02:54

Nucleosome Remodeling

9.1K
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...
9.1K
Histone Variants at the Centromere02:30

Histone Variants at the Centromere

4.3K
Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
4.3K
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

8.2K
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...
8.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Fusion-positive rhabdomyosarcoma oncofusions share a common interactome.

Nature communications·2026
Same author

A role of protein conformational dynamics in mammalian DNA methylation.

Structural dynamics (Melville, N.Y.)·2026
Same author

Structural insight into hierarchical DNMT3A autoinhibition and its dysregulation in disease.

Nature communications·2026
Same author

Stress-induced loss of CTCF reveals an alternative, promoter-based mode of cohesin looping.

bioRxiv : the preprint server for biology·2026
Same author

A Unified Model: Chromatin-Bound Multicomponent Condensates.

Cancer research·2026
Same author

Epigenetic priming promotes tyrosine kinase inhibitor resistance and oncogene amplification.

Nature structural & molecular biology·2025

Related Experiment Video

Updated: Jun 19, 2025

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
10:09

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

7.5K

Structural basis for the H2AK119ub1-specific DNMT3A-nucleosome interaction.

Xinyi Chen1, Yiran Guo2,3, Ting Zhao4

  • 1Department of Biochemistry, University of California, Riverside, CA, 92521, USA.

Nature Communications
|July 23, 2024
PubMed
Summary

DNA methyltransferase DNMT3A1 specifically binds to H2AK119ub1-modified nucleosomes. This structural insight reveals the molecular basis for DNA methylation establishment and its link to pathogenesis.

More Related Videos

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
06:32

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

1.8K
Analysis of Histone Antibody Specificity with Peptide Microarrays
09:47

Analysis of Histone Antibody Specificity with Peptide Microarrays

Published on: August 1, 2017

40.1K

Related Experiment Videos

Last Updated: Jun 19, 2025

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark
10:09

Isolation and Cultivation of Neural Progenitors Followed by Chromatin-Immunoprecipitation of Histone 3 Lysine 79 Dimethylation Mark

Published on: January 26, 2018

7.5K
Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique
06:32

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Published on: March 9, 2022

1.8K
Analysis of Histone Antibody Specificity with Peptide Microarrays
09:47

Analysis of Histone Antibody Specificity with Peptide Microarrays

Published on: August 1, 2017

40.1K

Area of Science:

  • Epigenetics
  • Structural Biology
  • Molecular Biology

Background:

  • DNA methyltransferase DNMT3A isoform 1 (DNMT3A1) is crucial for establishing DNA methylation patterns.
  • DNMT3A1 specifically recognizes H2AK119ub1-modified nucleosomes, but the molecular basis of this interaction is unknown.
  • Aberrant DNA methylation due to mis-regulation can lead to pathogenesis.

Purpose of the Study:

  • To elucidate the molecular basis of the DNMT3A1-nucleosome interaction.
  • To determine the structural mechanism of H2AK119ub1-dependent recruitment of DNMT3A1 to nucleosomes.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) to determine the structure of the DNMT3A1 UDR fragment complexed with H2AK119ub1-modified nucleosome.
  • Biochemical analyses to investigate the functional impact and competitive binding.

Main Results:

  • The cryo-EM structure reveals DNMT3A1 UDR binding extensively across the nucleosome surface, including H2AK119ub1, the H2A-H2B acidic patch, and DNA.
  • DNMT3A1 interaction with H2AK119ub1 influences DNMT3A1 cellular functionality.
  • Competition between DNMT3A1 and JARID2 for nucleosome binding suggests interplay between epigenetic pathways.

Conclusions:

  • A molecular basis for H2AK119ub1-dependent DNMT3A1-nucleosome association is reported.
  • This interaction is critical for DNMT3A1-mediated DNA methylation during development.
  • Findings highlight the interplay between DNA methylation and other epigenetic pathways like Polycomb repression.