9 results found
    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. 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
    2. Structural Biology and Molecular Biophysics

    Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima

    Ekaterina Morgunova, Yimeng Yin ... Jussi Taipale
    The epistasis observed in TF-DNA binding preferences can be explained by the presence of two optima of very similar Gibbs energy that are located relatively far from each other in sequence space.
    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. Plant Biology

    The plant pathogen Pseudomonas aeruginosa triggers a DELLA-dependent seed germination arrest in Arabidopsis

    Hicham Chahtane, Thanise Nogueira Füller ... Luis Lopez-Molina
    Arabidopsis seed germination can be repressed by a Pseudomonas factor.
    1. Developmental Biology
    2. Chromosomes and Gene Expression

    ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis

    Daniel M Cohen, Kyoung-Jae Won ... David J Steger
    The transcription factor C/EBPβ binds to different DNA sequences depending on whether it binds to ATF4, which enables C/EBPβ to conduct diverse transcriptional programs during adipocyte differentiation by exploiting an expanded motif repertoire.
    1. Chromosomes and Gene Expression

    Intergenerational epigenetic inheritance of cancer susceptibility in mammals

    Bluma J Lesch, Zuzana Tothova ... David C Page
    Genetic knockout of the histone demethylase Kdm6a in the mouse germ line leads to elevated cancer incidence in genetically wild type offspring.
    1. Structural Biology and Molecular Biophysics

    Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA

    Andrew John Knappenberger, Caroline Wetherington Reiss, Scott A Strobel
    RNA aptamers that are closely related and share a common scaffold can readily adapt to recognize new ligands through changes in just a few nucleotides.
    1. Cell Biology
    2. Computational and Systems Biology

    circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA

    Trine Line Hauge Okholm, Andreas Bjerregaard Kamstrup ... Christian Kroun Damgaard

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