8,541 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. 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. Structural Biology and Molecular Biophysics

    Structures of topoisomerase V in complex with DNA reveal unusual DNA-binding mode and novel relaxation mechanism

    Amy Osterman, Alfonso Mondragón
    Structural and biochemical studies explain the topoisomerase V DNA relaxation mechanism by showing that it adopts an unusual conformation when bound to DNA that exposes the active site.
    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. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA

    Claudia C Carcamo, Matthew F Poyton ... Taekjip Ha
    In vitro single-particle tracking reveals that ATP binding increases the one-dimensional diffusion of yeast chromatin remodeler SWR1 on DNA stretched between optical tweezers and diffusion is confined by protein roadblocks and nucleosomes.
    1. Structural Biology and Molecular Biophysics

    Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways

    Sukrit Suksombat, Rustem Khafizov ... Yann R Chemla
    Single-molecule force and fluorescence spectroscopy reveal the structural states and dynamics of E. coli single-stranded DNA binding proteins and the energy landscape of the nucleo–protein complex.
    1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog

    Antoine Hocher, Maria Rojec ... Tobias Warnecke
    In Thermoplasma acidophilum, an archaeon without histones, a DNA-binding protein acquired from bacteria via horizontal gene transfer mediates histone-like chromatin architecture.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Dissecting the DNA binding landscape and gene regulatory network of p63 and p53

    Konstantin Riege, Helene Kretzmer ... Martin Fischer
    A resource of p63-regulated genes, genomic loci bound by p63, p63 DNA recognition motifs, and potential co-factors is generated through a meta-analysis of high-throughput datasets.
    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    A novel single alpha-helix DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function

    Ruben Rosas, Rhiannon R Aguilar ... Mair EA Churchill
    The lysine/glutamic acid/arginine region in chromatin assembly factor (CAF-1) forms a long single alpha-helix DNA-binding domain, facilitating the recognition of tetrasome-length DNA and linking functional domains within the CAF-1 architecture for efficient tetrasome assembly after DNA synthesis.
    1. Chromosomes and Gene Expression

    Linker histone H1.8 inhibits chromatin binding of condensins and DNA topoisomerase II to tune chromosome length and individualization

    Pavan Choppakatla, Bastiaan Dekker ... Hironori Funabiki
    Linker histone H1.8 shapes mitotic chromosomes by tuning the number and size of condensin-dependent DNA loops and suppressing condensin and DNA topoisomerase II-dependent individualization.

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