1,927 results found
    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. Chromosomes and Gene Expression

    Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

    Davide M Coda et al.
    NODAL/Activin-induced SMAD2 binding directly drives remodeling of both open and closed chromatin and does not directly correlate with temporal patterns of gene expression upon prolonged signaling.
    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. Chromosomes and Gene Expression

    The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism

    Timothy J Parnell et al.
    A combination of genetics, expression, genomic localization, and genomic nucleosome profiling demonstrates antagonism between two chromatin remodelers that reveal different mechanisms at different promoter architectures.
    1. Chromosomes and Gene Expression

    The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1

    Peter J Skene et al.
    The ATP-dependent chromatin remodeler Chd1 controls nucleosome turnover to allow RNA Polymerase to transcribe in vivo.
    1. Chromosomes and Gene Expression

    Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation

    Steven Henikoff et al.
    A simple modification of CUT&Tag chromatin profiling method provides high-quality chromatin accessibility maps and indicates that 'open' chromatin results from a transcription-coupled process at promoters and enhancers.
    1. Developmental Biology
    2. Chromosomes and Gene Expression

    Chromatin signature of widespread monoallelic expression

    Anwesha Nag et al.
    Active and repressive chromatin marks, asymmetrically distributed between alleles, distinguish gene bodies subject to epigenetically controlled monoallelic expression on autosomes in human cells.
    1. Developmental Biology
    2. Neuroscience

    Neuroblast-specific open chromatin allows the temporal transcription factor, Hunchback, to bind neuroblast-specific loci

    Sonia Q Sen et al.
    Spatial factors generate neuroblast-specific open chromatin, thereby biasing the subsequent binding of transcription factors to produce neuroblast-specific neurons.
    1. Cell Biology
    2. Evolutionary Biology

    Chromatin is an ancient innovation conserved between Archaea and Eukarya

    Ron Ammar et al.
    Similarities in the way that nucleosomes are organized into chromatin in archaea and eukaryotes suggest that chromatin might have been involved in gene regulation before its role in DNA packaging evolved.
    1. Physics of Living Systems

    Mesoscale phase separation of chromatin in the nucleus

    Gaurav Bajpai et al.
    Computer simulations show transitions between novel types of chromatin organization (peripheral, central, conventional) depending on chromatin interactions with itself, the lamin and nuclear hydration, measured in recent experiments.

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