426 results found
    1. Computational and Systems Biology
    2. Chromosomes and Gene Expression

    Combinatorial bZIP dimers display complex DNA-binding specificity landscapes

    José A Rodríguez-Martínez et al.
    Cognate site identification uncovers the impact of combinatorial dimerization in specifying new DNA binding sites for human bZIP transcription factors and comprehensive specificity landscapes predict the impact of SNPs on bZIP binding at previously unannotated regulatory loci.
    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. Cancer Biology
    2. Cell Biology

    IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation

    Li Pan et al.
    Unbiased analyses highlight context-specific crosstalk between Notch, DNA damage response genes, and PP2A, and provide a roadmap for understanding how Notch induces squamous cell differentiation.
    1. Evolutionary Biology

    Molecular function limits divergent protein evolution on planetary timescales

    Mariam M Konaté et al.
    Orthologous proteins that continuously maintain the same molecular function do not usually diverge beyond a certain level of sequence and structural similarity.
    1. Chromosomes and Gene Expression

    CRISPRi is not strand-specific at all loci and redefines the transcriptional landscape

    Françoise S Howe et al.
    CRISPR interference (CRISPRi), which uses small guide RNAs to target catalytically dead Cas9 protein to chromatin, disrupts existing transcription units and generates new sites for initiation and termination of transcription on both strands of DNA.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads

    Huy Quoc Nguyen et al.
    A novel high-throughput method for measuring many weak protein-peptide affinities simultaneously reveals how calcineurin, a human phosphatase essential for the immune response, recognizes its peptide substrates.
    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

    PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells

    Shuchi Agrawal Singh et al.
    A key transcription-factor for osteogenic differentiation, PLZF, acts as a transcriptional activator by binding to active developmental enhancers and facilitates mediator recruitment, but is not involved in enhancer looping.
    1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    'Palaeoshellomics’ reveals the use of freshwater mother-of-pearl in prehistory

    Jorune Sakalauskaite et al.
    Ancient proteomes from tiny shell ornaments were successfully characterised for the first time, showing the unexpected use of mother-of-pearl from local riverine molluscs in both coastal and inland prehistoric sites.
    1. Microbiology and Infectious Disease

    Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites

    Juliane Fischer et al.
    Genome-wide chromatin mapping during bacterial-fungal cocultivation identifies the Myb-like transcription factor BasR as the major regulatory node of bacteria-triggered production of fungal secondary metabolites.

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