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Related Concept Videos

The Nucleosome Core Particle02:10

The Nucleosome Core Particle

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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...
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The Nucleosome Core Particle01:12

The Nucleosome Core Particle

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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...
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Position-effect Variegation02:32

Position-effect Variegation

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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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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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Heterochromatin02:38

Heterochromatin

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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 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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Nucleosome Remodeling02:54

Nucleosome Remodeling

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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.
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A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
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DPNuc: Identifying Nucleosome Positions Based on the Dirichlet Process Mixture Model.

Huidong Chen, Jihong Guan, Shuigeng Zhou

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |December 17, 2015
    PubMed
    Summary

    This study introduces DPNuc, a new computational method for precisely identifying nucleosome positions on chromosomes. DPNuc accurately detects nucleosome configurations, even with overlapping data, without needing prior knowledge.

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    Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
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    Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • Nucleosomes and linker DNA form chromatin, crucial for gene regulation, DNA replication, and repair.
    • Accurate nucleosome positioning is vital for understanding various genomic processes.
    • Current computational methods for nucleosome detection using ChIP-seq lack detail and require prior knowledge, limiting accuracy.

    Purpose of the Study:

    • To develop a novel computational approach for accurate and detailed nucleosome position identification.
    • To overcome limitations of existing methods, particularly in handling complex nucleosome configurations and noise.
    • To eliminate the need for prior knowledge about nucleosome size or number in detection algorithms.

    Main Methods:

    • Development of DPNuc, a method based on the Dirichlet process mixture model.
    • Utilizing Markov chain Monte Carlo (MCMC) simulations to determine the mixture model.
    • Comparative analysis against three existing nucleosome detection methods.

    Main Results:

    • DPNuc provides more detailed nucleosome information and reveals chromosomal configurations more accurately.
    • The method excels in identifying nucleosome positions in complex, overlapping scenarios.
    • DPNuc demonstrates superior performance, achieving a higher F-score on benchmark nucleosome maps.
    • The approach reliably detects nucleosome size distribution without prior input.

    Conclusions:

    • DPNuc offers a significant advancement in computational nucleosome mapping.
    • The method enhances the understanding of chromatin organization and its functional implications.
    • DPNuc provides a robust tool for genomic research requiring precise nucleosome positioning data.