2,032 results found
    1. Computational and Systems Biology

    Synthetic and genomic regulatory elements reveal aspects of cis-regulatory grammar in mouse embryonic stem cells

    Dana M King et al.
    The independent effects of transcription factor binding sites are large regardless of sequence context, but the interactions between sites are context dependent.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells

    Christopher D Todd et al.
    Genetic and epigenetic editing experiments establish causal links between transposon-derived enhancers and gene regulation in mouse embryonic and extraembryonic lineages.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Cis-regulatory basis of sister cell type divergence in the vertebrate retina

    Daniel P Murphy et al.
    While photoreceptor and bipolar cells exhibit very similar cis-regulatory grammars, subtle differences in homeodomain motif enrichment represent a key distinction driving the divergence in their transcriptomes.
    1. Computational and Systems Biology
    2. Chromosomes and Gene Expression

    An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability

    Judith Schütte et al.
    A computer model built on insights gained from comprehensive experimental analysis reveals mechanisms of blood stem cell regulation.
    1. Genetics and Genomics

    Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

    Benoit Ballester et al.
    Combinatorial transcription factor binding shared by multiple species enriches for essential biological pathways and coincides with disease-causing regulatory DNA mutations.
    1. Developmental Biology

    Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks

    Kelsey H Elliott et al.
    Context-dependent optimization of Gli-binding site occupancy, in the presence of Hand2, is critical for modulating tissue-specific transcriptional output within tissues that lack an obvious Hedgehog morphogen gradient.
    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. Developmental Biology
    2. Chromosomes and Gene Expression

    Multiple knockout mouse models reveal lincRNAs are required for life and brain development

    Martin Sauvageau et al.
    Long intergenic noncoding RNA molecules (lincRNAs) are shown to have critical roles in mammalian development and physiology in vivo.
    1. Developmental Biology

    A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation

    Meng Amy Li et al.
    A novel lncRNA (Ephemeron) is connected to known post-transcriptional and epigenetic regulators as part of an integrated machinery, which controls the timely exit from the naïve state of mouse embryonic stem cells.
    1. Computational and Systems Biology
    2. Developmental Biology

    A balance of positive and negative regulators determines the pace of the segmentation clock

    Guy Wiedermann et al.
    Computational modelling together with experimental manipulation indicate that the stability and turnover of activated Notch is inextricably linked to the regulation of the pace of segmentation clock gene expression in the presomitic mesoderm.

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