3,247 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, Aaron W Reinke ... Aseem Z Ansari
    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. Computational and Systems Biology

    Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE

    Todd R Riley, Allan Lazarovici ... Harmen J Bussemaker
    A biophysically principled algorithm can build quantitative models of protein-DNA binding specificity of unprecedented accuracy from a leading type of high-throughput in vitro binding data.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase

    Anna L Mallam, David J Sidote, Alan M Lambowitz
    The core domains of an RNA helicase interact with a wide variety of NTPs and nucleic acids suggesting how related enzymes may have evolved to have diverse functions.
    1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

    Kazuhiro R Nitta, Arttu Jolma ... Jussi Taipale
    Drosophila has almost all transcription factor binding specificities available to humans; and human transcription factors with divergent specificities operate in cell types that are not found in fruit flies.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Molecular basis for allosteric specificity regulation in class Ia ribonucleotide reductase from Escherichia coli

    Christina M Zimanyi, Percival Yang-Ting Chen ... Catherine L Drennan
    Substrate and effector bound structures of a bacterial ribonucleotide reductase reveal the molecular basis by which substrate preference is modulated by a distal site on the enzyme.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence

    Tingting Wang, Wenju Sun ... Jian Yan
    The transcription factor (TF)-binding specificities of Pseudomonas aeruginosa allow us to predict virulence-associated TFs and their target genes, which will facilitate to find effective treatment and prevention for its associated diseases.
    1. Biochemistry and Chemical Biology

    RNA binding to human METTL3-METTL14 restricts N6-deoxyadenosine methylation of DNA in vitro

    Shan Qi, Javier Mota ... Yogesh K Gupta
    Structured RNA elements bind to the human methyltransferase like-3 (METTL3)-METTL14 enzyme complex with high affinity and restrict the formation of N6-deoxymethyladenosine in DNA.
    1. Computational and Systems Biology
    2. Developmental Biology

    Tuned polymerization of the transcription factor Yan limits off-DNA sequestration to confer context-specific repression

    C Matthew Hope, Jemma L Webber ... Ilaria Rebay
    Tuned protein–protein interaction affinity optimizes the repressive function of the ETS family transcription factor Yan in order to contribute specificity and robustness to cell fate specification in the developing Drosophila eye.
    1. Evolutionary Biology

    Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

    Dave W Anderson, Alesia N McKeown, Joseph W Thornton
    Experimental mapping of the joint sequence space of an ancient transcription factor (TF) and its DNA binding sites reveals that epistasis across the molecular interface permitted the evolution of a new and specific TF-DNA complex.
    1. Genetics and Genomics
    2. Neuroscience

    Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms

    Yiqiao Zheng, Chi Sun ... Shiming Chen
    The integrated analysis of multi-omics and functional evidence both in vitro and in knock-in mouse models reveal novel gain-of-function pathogenic mechanisms of dominant CRX HD missense mutations.

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