5,088 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. 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. 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.
    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. 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

    Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

    Jeffrey M Alexander et al.
    Sox2 transcription is not correlated with spatial proximity of its essential regulatory enhancer in embryonic stem cells, suggesting gene transcription is not limited to periods of direct enhancer-promoter contact.
    1. Chromosomes and Gene Expression

    An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

    Peter J Skene, Steven Henikoff
    CUT&RUN (Cleavage Under Targets & Release Using Nuclease) profiles antibody-targeted DNA-binding proteins in situ with high resolution and low background, providing a simple, robust and scalable alternative to chromatin immunoprecipitation.
    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. Developmental Biology
    2. Plant Biology

    A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule

    Athul Vijayan et al.
    Deep imaging, machine-learning-based segmentation, and tissue annotation resulted in a developmental series of 3D digital ovules with cellular resolution allowing next-level analysis of the ontogenesis of this complex organ.

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