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Related Concept Videos

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. 
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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...
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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
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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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Protons and neutrons, collectively called nucleons, are packed together tightly in a nucleus. With a radius of about 10−15 meters, a nucleus is quite small compared to the radius of the entire atom, which is about 10−10 meters. Nuclei are extremely dense compared to bulk matter, averaging 1.8 × 1014 grams per cubic centimeter. If the earth’s density were equal to the average nuclear density, the earth’s radius would be only about 200 meters.
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Nuclear Fusion

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The process of converting very light nuclei into heavier nuclei is also accompanied by the conversion of mass into large amounts of energy, a process called fusion. The principal source of energy in the sun is a net fusion reaction in which four hydrogen nuclei fuse and ultimately produce one helium nucleus and two positrons.
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Related Experiment Video

Updated: Feb 6, 2026

The Use of Flow Cytometry to Assess the State of Chromatin in T Cells
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Nuclear cytometry and chromatin organization.

Paul J Smith1, Zbigniew Darzynkiewicz2, Rachel J Errington1

  • 1Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK.

Cytometry. Part a : the Journal of the International Society for Analytical Cytology
|August 26, 2018
PubMed
Summary

Nuclear probes and advanced cytometry reveal chromatin structure and compaction levels. Techniques like ChromEM tomography using DRAQ5™ offer new insights into DNA organization and cellular processes.

Keywords:
DNA damageDNA dyesDNA topoisomeraseDNA topologyDNA-targeted drugschromatinhistonesmicroscopynucleosomesselectron microscopysuper-resolution

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Deciphering High-Resolution 3D Chromatin Organization via Capture Hi-C
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Area of Science:

  • Cell Biology
  • Biophysics
  • Molecular Imaging

Background:

  • Nuclear probes are crucial for detecting and quantifying DNA in cells, aiding cytometry.
  • Current detection methods face limitations in resolution versus the volume of chromatin structures analyzed.
  • Understanding DNA compaction and its remodeling by probes/drugs is essential for cellular analysis.

Purpose of the Study:

  • To review nuclear and chromatin cytometry approaches for analyzing DNA organization.
  • To highlight the role of DNA-targeting probes and drugs in cellular studies.
  • To discuss advancements bridging scalar challenges in chromatin analysis.

Main Methods:

  • Exploration of various cytometry techniques, from traditional stains to fluorescent agents.
  • Application of super-resolution microscopy to enhance resolution and depth of analysis.
  • Utilizing ChromEM tomography with DRAQ5™ to visualize 3D chromatin structures.

Main Results:

  • Nuclear probes can report on chromatin order, disorder, and disruption by agents.
  • Specific probes, like DRAQ5™, reveal differences in local and global chromatin compaction.
  • Cytometric approaches are advancing the analysis of chromatin organization.

Conclusions:

  • Nuclear and chromatin cytometry, coupled with DNA probes, provides critical insights into cellular structure and function.
  • Advanced techniques like ChromEM tomography are key to overcoming resolution limitations.
  • Further development in cytometric approaches will enhance our understanding of genomic DNA organization and its modulation.