• Regulator proteins or symphonies of gene

    From ScienceDaily@1:317/3 to All on Tue Sep 21 21:30:38 2021
    Regulator proteins or symphonies of genes: Statistical modeling points
    way toward unified theory for DNA folding

    Date:
    September 21, 2021
    Source:
    American Institute of Physics
    Summary:
    Researchers seek to point a way toward a unified theory for how DNA
    changes shape when expressing genes. The scientists use an approach
    called statistical mechanics to explore the phenomenon of so-called
    expression waves of gene regulation. The group hopes to reconcile a
    long- standing gulf between the two scientific fields most involved
    in the topic, using concepts common to biology and physics.



    FULL STORY ==========================================================================
    At more than 2 meters long, the human DNA molecule uses intricate
    folding patterns to fit into cells while locally unfolding to express
    genes. Such phenomena, however, are difficult to measure in experiments,
    and theoretical frameworks explaining them continue to be at odds with
    one another.


    ========================================================================== Researchers in Italy, Japan, and Poland seek to point a way toward a
    unified theory for how DNA changes shape when expressing genes. Presenting their work in Biophysics Reviews, published by AIP Publishing, the
    scientists use an approach called statistical mechanics to explore the phenomenon of so-called expression waves of gene regulation.

    The group hopes to reconcile a long-standing gulf between the two
    scientific fields most involved in the topic.

    "Many scholars at the crossroad between physics and biology are now
    approaching what is probably the most crucial puzzle of biology," said co-author Alessandro Giuliani. "How is it possible that, starting from
    the same genetic background in the fertilized egg, around 400 highly differentiated cell types can arise, each endowed with a specific
    physiological role?" Biology-based theories often center on regulator proteins, called transcription factors, that biochemically conduct a
    symphony of genes to be expressed together. By contrast, many physicists
    have focused on expression waves, the rhythmic changes in expression
    levels across the genome, driven by relaxation and condensing of the
    DNA molecule itself.

    "It is something like the so-called hola, common in soccer and in other
    sport events, in which the spectators stand up simultaneously giving
    rise to a 'wave' spreading all over the stadium," Giuliani said.

    To get at the heart of the issue, the group focuses on a specific type
    of cell found in breast cancer with a proven track record of consistently behaving the same way to stimuli.

    They used statistical mechanics to make sense of how DNA molecules fold by assessing the collective behavior of a huge number of microscopic players
    in terms of ensemble properties, unlike classical top-down perspectives,
    like Newton's laws.

    Ultimately, the researchers landed in favor of expression waves,
    acknowledging that while transcription factors play a vital role, they
    are second fiddle to the changing shape of DNA.

    To unify these two perspectives, the authors present their conclusion
    using concepts common to biology and physics, limiting the use of
    mathematics to intuitive approaches such as recurrence quantification
    analysis and the classical statistical method of principal component
    analysis.

    Next, they look to apply the same approach to identify ecological tipping points based on the makeup of species in particular habitats.

    ========================================================================== Story Source: Materials provided by American_Institute_of_Physics. Note: Content may be edited for style and length.


    ========================================================================== Journal Reference:
    1. Giovanna Zimatore, Masa Tsuchiya, Midori Hashimoto, Andrzej
    Kasperski,
    Alessandro Giuliani. Self-organization of whole-gene expression
    through coordinated chromatin structural transition. Biophysics
    Reviews, 2021; 2 (3): 031303 DOI: 10.1063/5.0058511 ==========================================================================

    Link to news story: https://www.sciencedaily.com/releases/2021/09/210921172713.htm

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