2,708 results found
    1. Chromosomes and Gene Expression
    2. Physics of Living Systems

    Chromosome organization by one-sided and two-sided loop extrusion

    Edward J Banigan et al.
    Seemingly contradictory findings of single-molecule and in vivo experiments on a major mechanism of chromosome organization are reconciled by computationally investigating mechanisms of loop extrusion that are consistent with both.
    1. Chromosomes and Gene Expression
    2. Physics of Living Systems

    The interplay between asymmetric and symmetric DNA loop extrusion

    Edward J Banigan, Leonid A Mirny
    Models of chromosome compaction by condensins demonstrate that two-sided loop extrusion and long residence times are required for high compaction, suggesting a tight coupling between these two properties in vivo.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    A Brownian ratchet model for DNA loop extrusion by the cohesin complex

    Torahiko L Higashi et al.
    A structure-based model of the chromosomal cohesin complex, accompanied by molecular-mechanistic simulations, explains cohesin's key role in topologically entrapping DNA, as well as its ability to alternatively extrude DNA loops.
    1. Structural Biology and Molecular Biophysics
    2. Chromosomes and Gene Expression

    Compaction and segregation of sister chromatids via active loop extrusion

    Anton Goloborodko et al.
    Loop extrusion can robustly compact, segregate and disentangle mammalian chromosomes, suggesting it is a universal mechanism of genome folding during cell division.
    1. Chromosomes and Gene Expression
    2. Microbiology and Infectious Disease

    A low Smc flux avoids collisions and facilitates chromosome organization in Bacillus subtilis

    Anna Anchimiuk et al.
    Bacterial chromosome folding by DNA loop extrusion is here shown to rely on avoidance of SMC collisions by low SMC abundance, clustering of loading sites, efficient translocation, and rare unloading.
    1. Cell Biology
    2. Chromosomes and Gene Expression

    Cohesin and condensin extrude DNA loops in a cell cycle-dependent manner

    Stefan Golfier et al.
    Reconstitution of DNA loop extrusion in cellular contexts using Xenopus egg extracts shows that condensin extrudes DNA loops non-symmetrically in metaphase, whereas cohesin extrudes DNA loops symmetrically in interphase.
    1. Chromosomes and Gene Expression

    Scc2/Nipbl hops between chromosomal cohesin rings after loading

    James Rhodes et al.
    The cohesin loading factor Scc2/Nipbl interacts frequently with cohesin after the loading reaction in a manner consistent with a role in stimulating loop extrusion.
    1. Developmental Biology

    A complex regulatory landscape involved in the development of mammalian external genitals

    Ana Rita Amândio et al.
    In vertebrates, large regulatory landscapes sometimes behave as coherent regulatory units, which may explain the lack of effect sometimes observed when single enhancer sequences are deleted in isolation.
    1. Biochemistry and Chemical Biology
    2. Chromosomes and Gene Expression

    Determining cellular CTCF and cohesin abundances to constrain 3D genome models

    Claudia Cattoglio et al.
    Absolute quantification of CTCF and cohesin reveals quantitative constraints on 3D genome organization and illuminates the molecular architecture of the cohesin complex.
    1. Chromosomes and Gene Expression
    2. Computational and Systems Biology

    Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver

    Bryan J Matthews, David J Waxman
    Certain types of 3D chromatin loops are easy to predict from existing or easily obtainable 2D information, which benefits gene expression studies in tissues/cells/organisms without extensive pre-existing 3D information.

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