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

Heterochromatin02:38

Heterochromatin

17.8K
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...
17.8K
Chromatin Packaging02:21

Chromatin Packaging

21.2K
Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
21.2K
Chromatin Packaging01:32

Chromatin Packaging

18.8K
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
18.8K

You might also read

Related Articles

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

Sort by
Same author

Positive-Strand RNA Viral RdRps: From Structure Conservation and Activity Assay to Drug Development.

Molecules (Basel, Switzerland)·2026
Same author

The GmCYCLOPS paralogs regulate soybean nodulation and exhibit signatures during domestication.

Plant science : an international journal of experimental plant biology·2026
Same author

Recent advances in microfluidic technologies for circulating tumor cell isolation: from separation strategies to clinical translation.

Analytical methods : advancing methods and applications·2026
Same author

Advancing Normal Tissue Complication Probability Modeling with Supervised Contrastive Learning for Predicting Osteoradionecrosis.

Proceedings of the ... Symposium on Applied Computing. Symposium on Applied Computing·2026
Same author

Disentangling polymer confinement from specific-folding interactions reveals the drivers of <i>E. coli</i> chromosome organization.

bioRxiv : the preprint server for biology·2026
Same author

Spectroscopy-informed XANES-PXRD framework for multi-property prediction and structure inference.

Chemical science·2026
Same journal

Complex Indel Detection: A Simulation-Based Framework and Parsing with FreeBayes.

bioRxiv : the preprint server for biology·2026
Same journal

Emulating the gingival-tooth interface during bacterial, fungal, and viral infection in a microphysiological model of the human oral cavity.

bioRxiv : the preprint server for biology·2026
Same journal

Local SNP-explained methylation variation reveals genetically anchored and exposure-associated methylation architecture in the human brain.

bioRxiv : the preprint server for biology·2026
Same journal

Perinatal Semaglutide Treatment Improves Maternal Health and Mitigates Offspring Metabolic Dysfunction in a Mouse Model of Maternal Obesity.

bioRxiv : the preprint server for biology·2026
Same journal

Pervasive cryptic selection in the human noncoding genome.

bioRxiv : the preprint server for biology·2026
Same journal

Secreted ORF8 reprograms macrophages to enhance SARS-CoV-2 infection of lung epithelial cells.

bioRxiv : the preprint server for biology·2026
See all related articles
  1. Home
  3. Chrompolymerdb: A High-resolution Database Of Single-cell 3d Chromatin Structures For Functional Genomics.
  1. Home
  3. Chrompolymerdb: A High-resolution Database Of Single-cell 3d Chromatin Structures For Functional Genomics.

Related Experiment Video

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

4.3K

ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Structures for Functional Genomics.

Min Chen1, Lin Du2, Siyuan Zhao3

  • 1State Key Laboratory of Systems Medicine for Cancer and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.

Biorxiv : the Preprint Server for Biology
|November 19, 2025

View abstract on PubMed

Summary
This summary is machine-generated.

Researchers developed a new computational framework, Sequential Bayesian Inference Framework (sBIF), to reconstruct single-cell 3D chromatin structures from bulk Hi-C data. This enables detailed analysis of genome architecture and gene regulation across diverse cell types.

More Related Videos

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

411.4K
Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos
10:35

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

Published on: October 3, 2018

21.4K

Related Experiment Videos

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

4.3K
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
22:27

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

411.4K
Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos
10:35

Generation of Genome-wide Chromatin Conformation Capture Libraries from Tightly Staged Early Drosophila Embryos

Published on: October 3, 2018

21.4K

Area of Science:

  • Genomics
  • Computational Biology
  • Structural Biology

Background:

  • The 3D chromatin organization is crucial for gene regulation and genome stability.
  • Population-averaged assays like Hi-C obscure crucial single-cell conformational heterogeneity.
  • Understanding single-cell genome architecture is vital for deciphering gene regulation.

Purpose of the Study:

  • To develop a computational framework for deconvoluting bulk Hi-C data into single-cell 3D chromatin conformations.
  • To create a comprehensive, high-resolution database of single-cell chromatin structures.
  • To provide tools for exploring the relationship between 3D genome structure and biological processes.

Main Methods:

  • Developed the Sequential Bayesian Inference Framework (sBIF), a polymer physics-based modeling approach.
  • Applied sBIF to deconvolve population-averaged Hi-C data to reconstruct single-cell chromatin structures.
  • Created ChromPolymerDB, a publicly accessible database storing ~10^8 reconstructed 5 kb-resolution single-cell structures.

    • Main Results:

    • Successfully reconstructed ~10^8 single-cell 3D chromatin conformations at 5 kb resolution.
    • ChromPolymerDB encompasses over 60,000 genomic loci across 50 human cell types and conditions.
    • The database provides an interactive platform for 3D structural analysis and multi-omics integration.

    Conclusions:

    • ChromPolymerDB offers a unique resource for studying genome architecture and gene regulation at the single-cell level.
    • The platform facilitates comparative analyses of chromatin structure across different cell types, developmental stages, and disease contexts.
    • This work advances the field of comparative 3D genomics by providing unprecedented insights into genome organization.