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Related Concept Videos

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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Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also...
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Lampbrush Chromosomes01:51

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In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps.
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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
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Chromosome Structure02:40

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A functional eukaryotic chromosome must contain three elements: a centromere, telomeres, and numerous origins of replication.
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Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
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Chromatin 3D Reconstruction from Chromosomal Contacts Using a Genetic Algorithm.

Viacheslav Kapilevich, Shigeto Seno, Hideo Matsuda

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    |July 12, 2018
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    Summary
    This summary is machine-generated.

    This study introduces a new genetic algorithm to improve chromatin structure modeling from 3C data, enhancing accuracy over existing methods like ShRec3D for better gene regulation insights.

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    Area of Science:

    • Epigenetics and Genomics
    • Computational Biology
    • Molecular Biology

    Background:

    • Chromatin conformation is crucial for gene regulation.
    • Chromosome Conformation Capture (3C) technology enables analysis of 3D chromatin organization.
    • Existing algorithms for 3D chromatin reconstruction from 3C data have limitations.

    Purpose of the Study:

    • To address errors in ShRec3D's shortest path algorithm for chromatin modeling.
    • To develop an improved algorithm for more accurate 3D chromatin structure reconstruction.
    • To enhance the fidelity of chromatin models derived from 3C experimental data.

    Main Methods:

    • Proposed an improved algorithm optimizing shortest path distances using a genetic algorithm.
    • Compared the novel algorithm against ShRec3D using in silico 3C experimental data.
    • Evaluated model similarity and computational time for both algorithms.

    Main Results:

    • The proposed genetic algorithm approach significantly improved the similarity between the reconstructed model and the original chromatin structure.
    • The enhanced algorithm demonstrated superior accuracy compared to ShRec3D.
    • The increase in calculation time was reasonable, maintaining practical usability.

    Conclusions:

    • The genetic algorithm-based approach offers a more accurate method for 3D chromatin structure reconstruction from 3C data.
    • This improvement aids in a better understanding of the relationship between chromatin conformation and gene regulation.
    • The optimized algorithm provides a valuable tool for epigenetics research.