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Related Concept Videos

Chromatin Packaging02:21

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, 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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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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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)
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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
The writer...
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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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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Related Experiment Video

Updated: Jan 28, 2026

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

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A library-based method to rapidly analyse chromatin accessibility at multiple genomic regions.

Asjad Basheer1, Harald Berger, Yazmid Reyes-Dominguez

  • 1Austrian Research Centers, Department of Applied Genetics and Cell Biology, BOKU University Vienna, Vienna, Austria.

Nucleic Acids Research
|March 3, 2009
PubMed
Summary

This study introduces a novel method for analyzing chromatin accessibility across the genome, enabling locus-specific DNA fragment analysis from condition-specific libraries. This approach overcomes limitations of traditional and high-throughput techniques for studying gene regulation.

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Last Updated: Jan 28, 2026

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Traditional chromatin analysis is locus-specific or uses varied templates, hindering standardized analysis of large genomic regions or co-regulated genes.
  • Genome-wide chromatin accessibility mapping is data-intensive, costly, and limits sample analysis.

Purpose of the Study:

  • To develop a method bridging traditional and high-throughput approaches for chromatin analysis.
  • To enable condition-specific, genome-wide chromatin fragment library production for locus-specific analysis.
  • To validate the method using known gene promoters and study nucleosomal positioning.

Main Methods:

  • Production of condition-specific, genome-wide chromatin fragment libraries.
  • Locus-specific DNA fragment analysis using these libraries.
  • Validation using the promoters of niiA and niaD genes in Aspergillus.
  • Application to study nucleosomal positioning at areA and aflR gene promoters.

Main Results:

  • Successfully developed and validated a novel chromatin analysis method.
  • Demonstrated the utility of condition-specific libraries for locus-specific analysis.
  • Provided insights into nucleosomal positioning at key regulatory loci.

Conclusions:

  • The developed method offers a standardized and efficient approach for chromatin analysis.
  • It bridges the gap between traditional and high-throughput techniques, facilitating the study of gene regulation.
  • Applicable for investigating chromatin dynamics in specific biological conditions.