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

Chromatin Packaging02:21

Chromatin Packaging

23.3K
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...
23.3K
Chromatin Packaging01:32

Chromatin Packaging

20.3K
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...
20.3K
Chromatin Packaging02:21

Chromatin Packaging

10.3K
10.3K
Lampbrush Chromosomes01:51

Lampbrush Chromosomes

8.9K
In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps.
LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops...
8.9K
Lampbrush Chromosomes01:51

Lampbrush Chromosomes

3.1K
3.1K
Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

7.6K
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...
7.6K

You might also read

Related Articles

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

Sort by
Same author

Large-scale data-driven pre-trained DNA models enhance performance across diverse genomics tasks.

Nature communications·2026
Same author

Avian lung single-cell atlas elucidates evolutionary divergence in endothermic respiration.

Molecular biology and evolution·2026
Same author

HRCHY-CytoCommunity identifies hierarchical tissue organization in cell-type spatial maps.

Nature communications·2026
Same author

Multi-species integration, alignment and annotation of single-cell RNA-seq data with CAMEX.

Nature communications·2026
Same author

Bridging cancer cell-intrinsic driver genes and -extrinsic cell-cell communication with Driver2Comm.

PLoS computational biology·2026
Same author

De novo covalent drug generation with enhanced drug-likeness and safety.

Communications biology·2026
Same journal

Demonstration of a quantum C-NOT gate in a time-multiplexed fully reconfigurable photonic processor.

Nature communications·2026
Same journal

Nonlinear quantum light source with van der Waals ferroelectric NbOX<sub>2</sub> (X = Br, I).

Nature communications·2026
Same journal

Antagonistic histone H2A variants and autonomous heterochromatin formation shape epigenomic patterns in Arabidopsis.

Nature communications·2026
Same journal

The long tail of nitrate pollution in groundwater challenges governance of global water quality.

Nature communications·2026
Same journal

Select microbial metabolites promote tau aggregation in a murine tauopathy model.

Nature communications·2026
Same journal

Warming climate has lengthened global intense tropical cyclone seasons.

Nature communications·2026
See all related articles

Related Experiment Video

Updated: Apr 8, 2026

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

4.8K

CellLoop: Identifying single-cell 3D genome chromatin loops.

Yusen Ye1, Yiheng Wang2, Shiji Liu2

  • 1School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China. ysye@xidian.edu.cn.

Nature Communications
|April 6, 2026
PubMed
Summary
This summary is machine-generated.

CellLoop identifies single-cell chromatin loops by integrating cell contacts, improving loop detection and revealing cell-specific loops. This computational framework enhances understanding of 3D genome organization in individual cells.

More Related Videos

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
11:25

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

11.1K
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

412.4K

Related Experiment Videos

Last Updated: Apr 8, 2026

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

4.8K
3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells
11:25

3D Multicolor DNA FISH Tool to Study Nuclear Architecture in Human Primary Cells

Published on: January 25, 2020

11.1K
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

412.4K

Area of Science:

  • Genomics
  • Computational Biology
  • Epigenetics

Background:

  • Single-cell 3D genome technologies offer insights into chromatin architecture.
  • Challenges include data sparsity and noise, hindering robust chromatin loop detection at the single-cell level.

Purpose of the Study:

  • To present CellLoop, a computational framework for identifying chromatin loops from single-cell contact data.
  • To improve the accuracy and scalability of chromatin loop detection in individual cells.

Main Methods:

  • CellLoop integrates intra-cellular and neighboring inter-cellular contacts using a density-based voting strategy.
  • The framework was applied to Dip-C, HiRES, GAGE-seq, and MERFISH datasets.

Main Results:

  • CellLoop demonstrated improved loop detection in mouse brain data, consistent with spatial organization.
  • It revealed single-cell-specific chromatin loops linked to transcriptional regulation and cell identity.
  • CellLoop facilitated finer cell subtype delineation in embryogenesis data by mitigating cell cycle effects.
  • Integration with other data types redefined spatial domain functions through chromatin loop dynamics.

Conclusions:

  • CellLoop offers a scalable and accurate method for characterizing chromatin loop variability at single-cell resolution.
  • The study highlights the importance of 3D genome features in interpreting transcriptional and spatial heterogeneity.