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Related Concept Videos

The Nucleosome Core Particle02:10

The Nucleosome Core Particle

Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
The Nucleosome Core Particle01:12

The Nucleosome Core Particle

Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
Nucleosome Remodeling02:54

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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 timing and level of...
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
Position-effect Variegation02:32

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.

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Related Experiment Video

Updated: May 8, 2026

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

A comparative evaluation on prediction methods of nucleosome positioning.

Hui Liu, Ruichang Zhang, Wei Xiong

    Briefings in Bioinformatics
    |September 12, 2013
    PubMed
    Summary

    Computational models predict nucleosome positioning, crucial for DNA accessibility. The latest thermodynamic models offer steadier performance across species, though accuracy decreases from yeast to humans.

    Keywords:
    G:C contentnucleosomal sequencenucleosome positioningperformance comparisonprediction accuracy

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • Nucleosome positioning regulates DNA accessibility, impacting cellular processes like transcription and replication.
    • Numerous computational models exist to predict genome-wide nucleosome positions from DNA sequences.
    • Comparative analysis of predicted and experimental maps aids in understanding gene regulation.

    Purpose of the Study:

    • To conduct a comprehensive performance comparison of eight widely used computational methods for nucleosome positioning prediction.
    • To evaluate these methods across four diverse species: yeast, fruitfly, mouse, and human.
    • To assess performance on specific genomic regions, including gene sequences, promoters, and 5'UTR exons.

    Main Methods:

    • Performance comparison of eight computational nucleosome positioning prediction methods.
    • Application of methods to DNA sequences from yeast, fruitfly, mouse, and human.
    • Analysis of prediction accuracy across different genomic regions (genes, promoters, 5'UTR exons).

    Main Results:

    • The two latest versions of the thermodynamic model demonstrated steadier performance compared to other methods evaluated.
    • All tested methods were workable across the four species.
    • Prediction performance generally decreased from yeast to human, suggesting conserved but increasingly complex regulatory mechanisms.

    Conclusions:

    • The thermodynamic model variants show robust and consistent performance in nucleosome positioning prediction.
    • Nucleosome positioning mechanisms are conserved across evolution but become more complex in higher eukaryotes.
    • This comparative evaluation aids researchers in selecting appropriate computational tools for nucleosome positioning studies.