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Related Concept Videos

Heterochromatin02:38

Heterochromatin

14.7K
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...
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Chromatin Packaging01:32

Chromatin Packaging

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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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Euchromatin01:01

Euchromatin

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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...
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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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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...
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Duplication of Chromatin Structure02:05

Duplication of Chromatin Structure

6.1K
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...
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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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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...
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Related Experiment Video

Updated: Sep 24, 2025

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

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Extensive Chromatin Structure-Function Associations Revealed by Accurate 3D Compartmentalization Characterization.

Zi Wen1,2, Weihan Zhang1, Quan Zhong1,2

  • 1Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.

Frontiers in Cell and Developmental Biology
|May 6, 2022
PubMed
Summary

We introduce MOSAIC, a new method to identify genome compartments. MOSAIC reveals dynamic micro-compartments, improving our understanding of gene regulation and disease.

Keywords:
A/B compartmentchromatin architectureheterochromatinmodularitytranscriptional regulation

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

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Area of Science:

  • Genomics
  • Molecular Biology
  • Computational Biology

Background:

  • Hi-C data reveals A/B compartments correlating with euchromatin and heterochromatin.
  • The standard A/B compartment model leaves many genomic regions ambiguously classified.
  • Accurate chromatin state identification is crucial for understanding gene regulation.

Purpose of the Study:

  • To develop MOSAIC (MOdularity and Singular vAlue decomposition-based Identification of Compartments), a novel computational method for precise detection of genome compartmental states.
  • To identify and characterize novel compartmental states beyond the traditional A/B classification.
  • To explore the dynamic nature and functional implications of these newly identified compartments.

Main Methods:

  • Development of MOSAIC, a method employing modularity and singular value decomposition for compartmental state detection.
  • Application of MOSAIC to Hi-C data from human cell lines (GM12878 and K562).
  • Analysis of gene expression data in conjunction with compartmental states to identify structure-function relationships.

Main Results:

  • MOSAIC accurately identifies compartmental states, including previously ambiguous regions.
  • Two new compartmental states, termed micro-compartments, are discovered, covering approximately 30% of the genome.
  • Micro-compartments are highly dynamic across different cell types and are associated with specific gene loci (e.g., CD86, ILDR1, GATA2) showing concordance with gene expression.

Conclusions:

  • MOSAIC provides a more refined view of genome organization by uncovering micro-compartments.
  • These fine-scale, dynamic compartmental states play a significant role in transcriptional regulation.
  • Distinguishing micro-compartments is essential for accurate characterization of chromatin structure-function relationships and understanding disease mechanisms.