4,620 results found
    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

    Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci

    Daan Noordermeer et al.
    Hox genes are activated sequentially and, at the same time, undergo a transition from an inactive to an active chromatin compartment, most likely to prevent posterior genes being activated too early.
    1. Genetics and Genomics

    Beyond the RNA-dependent function of LncRNA genes

    Tamer Ali, Phillip Grote
    Recent examples demonstrate that already the transcriptional activity at lncRNA genes does have an important function on gene regulation, while the produced non-coding RNA might be dispensable.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Spatial inter-centromeric interactions facilitated the emergence of evolutionary new centromeres

    Krishnendu Guin et al.
    Proximity and homology guided inter-chromosomal translocations drive karyotype evolution.
    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.
    1. Computational and Systems Biology
    2. Developmental Biology

    MorphoGraphX: A platform for quantifying morphogenesis in 4D

    Pierre Barbier de Reuille et al.
    MorphoGraphX summarizes full 3D datasets as curved surface images (2.5D), enabling the efficient quantification of growth and gene expression data from large time-lapse volumetric datasets.
    1. Stem Cells and Regenerative Medicine

    Cohesin controls intestinal stem cell identity by maintaining association of Escargot with target promoters

    Aliaksandr Khaminets et al.
    Cohesin-regulated 3D genome conformation controls activity of transcription factor Escargot in intestinal stem cells, prevents premature differentiation into enterocytes and maintains intestinal homeostasis.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    A combination of transcription factors mediates inducible interchromosomal contacts

    Seungsoo Kim et al.
    A pooled mutational scanning approach for 3D chromosome conformation reveals how multiple transcription factors can jointly specify condition-specific genome conformations.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

    Martial Marbouty et al.
    A technique called meta3C provides an elegant and integrated approach to metagenomic analysis by allowing the de novo assembly, scaffolding and 3D characterization of unknown genomes from a complex mix of species
    1. Structural Biology and Molecular Biophysics
    2. Chromosomes and Gene Expression

    3D imaging of Sox2 enhancer clusters in embryonic stem cells

    Zhe Liu et al.
    Lattice light-sheet single-molecule imaging shows 3D Sox2 enhancer clusters in live embryonic stem cells and reveals a model linking 3D spatial distribution of cis-elements, differential target search features and localized gene regulation.

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