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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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 is an enzyme that can...
Heterochromatin02:38

Heterochromatin

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 9th...
Histone Modification02:32

Histone Modification

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 deacetylase,...
Chromatin Packaging02:21

Chromatin Packaging

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 structures.
Chromatin Packaging01:32

Chromatin Packaging

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...

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Related Experiment Video

Updated: May 7, 2026

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

Revealing long-range interconnected hubs in human chromatin interaction data using graph theory.

R E Boulos1, A Arneodo, P Jensen

  • 1Université de Lyon, F-69000 Lyon, France and Laboratoire de Physique, ENS de Lyon, CNRS UMR5672, F-69007 Lyon, France.

Physical Review Letters
|October 1, 2013
PubMed
Summary

Graph theory reveals master replication origins in the human genome as network hubs. Analyzing chromatin interaction data (Hi-C), this study identifies key DNA loci central to genome organization and function.

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Last Updated: May 7, 2026

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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Published on: May 6, 2010

Associated Chromosome Trap for Identifying Long-range DNA Interactions
14:49

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Published on: April 23, 2011

In-Nucleus Hi-C in Drosophila Cells
11:58

In-Nucleus Hi-C in Drosophila Cells

Published on: September 15, 2021

Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology
  • Network Science

Background:

  • Understanding the three-dimensional (3D) organization of the human genome is crucial for deciphering its functions.
  • Chromatin interaction data, such as Hi-C, provides insights into the spatial proximity of DNA regions.
  • Identifying functional genomic elements like replication origins is key to understanding genome dynamics.

Purpose of the Study:

  • To apply graph theory principles to analyze human genome chromatin interaction data.
  • To investigate the relationship between network properties and functional genomic features, specifically master replication origins.
  • To explore the potential of graph theory in modeling nuclear organization and discriminating between polymer models.

Main Methods:

  • Utilized graph theory to model the human genome based on Hi-C data.
  • Calculated network centrality measures for DNA loci.
  • Correlated network centrality with the identification of master replication origins.

Main Results:

  • Identified 'master' replication origins as DNA loci exhibiting maximal network centrality.
  • Demonstrated that these master origins form interconnected hubs within and between chromosomes.
  • Established a quantitative link between genomic network structure and replication origin function.

Conclusions:

  • Graph theory provides a powerful framework for analyzing genome structure and function from Hi-C data.
  • Master replication origins represent critical network hubs in the human genome's 3D organization.
  • This approach offers quantitative insights valuable for understanding nuclear organization and polymer models.