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

Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

6.8K
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...
6.8K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

24.0K
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...
24.0K
Heterochromatin02:38

Heterochromatin

15.0K
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...
15.0K
Euchromatin01:01

Euchromatin

7.9K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
7.9K
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

6.2K
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...
6.2K
Histone Modification02:32

Histone Modification

14.7K
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...
14.7K

You might also read

Related Articles

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

Sort by
Same author

Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes.

bioRxiv : the preprint server for biology·2026
Same author

Emergent Isotropic-Nematic Transition in 3D Semiflexible Active Polymers.

Physical review letters·2026
Same author

Emergent domain segregation in self-interacting polymers explains chromosome 3D conformations in single human cells.

Physical review. E·2026
Same author

Physics-Based Modeling of Sparse Single-Cell Hi-C Uncovers Structural and Epigenetic Variability.

International journal of molecular sciences·2026
Same author

Supporting-like cells constitute an alternative steroidogenic lineage conserved in amniotes.

bioRxiv : the preprint server for biology·2026
Same author

Heterogeneity and dynamics of DENV-specific CD8 + T cells in dengue infection.

Nature communications·2026

Related Experiment Video

Updated: Oct 13, 2025

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

3.8K

Cell-type specialization is encoded by specific chromatin topologies.

Warren Winick-Ng1, Alexander Kukalev2, Izabela Harabula2,3

  • 1Max-Delbrück Centre for Molecular Medicine, Berlin Institute for Medical Systems Biology, Epigenetic Regulation and Chromatin Architecture Group, Berlin, Germany. warren.winick-ng@mdc-berlin.de.

Nature
|November 18, 2021
PubMed
Summary
This summary is machine-generated.

We developed immunoGAM to map 3D chromatin structure in specific brain cell types without tissue disruption. This method reveals how chromatin organization relates to gene expression and specialized neuronal functions.

More Related Videos

TChIP-Seq: Cell-Type-Specific Epigenome Profiling
07:28

TChIP-Seq: Cell-Type-Specific Epigenome Profiling

Published on: January 23, 2019

8.0K
HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.5K

Related Experiment Videos

Last Updated: Oct 13, 2025

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
09:32

Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C

Published on: October 14, 2022

3.8K
TChIP-Seq: Cell-Type-Specific Epigenome Profiling
07:28

TChIP-Seq: Cell-Type-Specific Epigenome Profiling

Published on: January 23, 2019

8.0K
HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.5K

Area of Science:

  • Genomics and Molecular Biology
  • Neuroscience
  • Epigenetics

Background:

  • Three-dimensional (3D) chromatin structure is crucial for gene regulation and cell function.
  • Existing chromatin conformation capture methods have limitations in mapping neuronal systems, particularly regarding dynamic changes and cell-type specificity without tissue dissociation.

Purpose of the Study:

  • To develop and apply a novel method, immunoGAM, for mapping 3D chromatin topology genome-wide in specific brain cell types from single animals without tissue disruption.
  • To investigate the relationship between cell-type specialized 3D chromatin structures and gene expression patterns in the brain.

Main Methods:

  • ImmunoGAM, an extension of genome architecture mapping (GAM), utilizes ligation-free technology on nuclear cryosections to map genome topology.
  • It enables cell-type selection from complex tissues using low cell numbers (approx. 1,000 cells) and avoids tissue dissociation.
  • Chromatin interactions are identified by analyzing the co-segregation probability of DNA loci across nuclear slices.

Main Results:

  • Cell-type specialized 3D chromatin structures were mapped at multiple genomic scales, correlating with gene expression patterns.
  • Extensive 'melting' of long genes was observed during high expression and/or high chromatin accessibility.
  • Neuron subtype-specific contacts involve genes related to addiction and synaptic plasticity, with transcription factor binding sites in accessible chromatin.
  • Sensory receptor genes were found in heterochromatic compartments, forming long-range contacts.

Conclusions:

  • ImmunoGAM provides a powerful tool for studying 3D chromatin organization in specific brain cell types at single-animal resolution.
  • Specific chromatin conformations in brain cells are intricately linked to gene regulation mechanisms and specialized cellular functions.
  • The findings highlight the importance of 3D genome architecture in neuronal cell identity and function.