title: ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors.
abstract: The classical DNA recognition sequence of the glucocorticoid receptor (GR) appears to be present at only a fraction of bound genomic regions. To identify sequences responsible for recruitment of this transcription factor (TF) to individual loci, we turned to the high-resolution ChIP-exo approach. We exploited this signal by determining footprint profiles of TF binding at single-base-pair resolution using ExoProfiler, a computational pipeline based on DNA binding motifs. When applied to our GR and the few available public ChIP-exo data sets, we find that ChIP-exo footprints are protein- and recognition sequence-specific signatures of genomic TF association. Furthermore, we show that ChIP-exo captures information about TFs other than the one directly targeted by the antibody in the ChIP procedure. Consequently, the shape of the ChIP-exo footprint can be used to discriminate between direct and indirect (tethering to other DNA-bound proteins) DNA association of GR. Together, our findings indicate that the absence of classical recognition sequences can be explained by direct GR binding to a broader spectrum of sequences than previously known, either as a homodimer or as a heterodimer binding together with a member of the ETS or TEAD families of TFs, or alternatively by indirect recruitment via FOX or STAT proteins. ChIP-exo footprints also bring structural insights and locate DNA:protein cross-link points that are compatible with crystal structures of the studied TFs. Overall, our generically applicable footprint-based approach uncovers new structural and functional insights into the diverse ways of genomic cooperation and association of TFs.
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
authors.forename: Stephan R
authors.initials: SR
authors.lastname: Starick
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale, U1024, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, F-75005 Paris, France.
authors.forename: Jonas
authors.initials: J
authors.lastname: Ibn-Salem
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
authors.forename: Marcel
authors.initials: M
authors.lastname: Jurk
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale, U1024, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, F-75005 Paris, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Hernandez
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
authors.forename: Michael I
authors.initials: MI
authors.lastname: Love
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
authors.forename: Ho-Ryun
authors.initials: HR
authors.lastname: Chung
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale, U1024, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, F-75005 Paris, France.
authors.forename: Morgane
authors.initials: M
authors.lastname: Thomas-Chollier
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
authors.forename: Sebastiaan H
authors.initials: SH
authors.lastname: Meijsing
mesh_terms: D000076246:CCCTC-Binding Factor; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology; D047628:Estrogen Receptor alpha / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D056426:Genetic Loci; D023281:Genomics; D006367:HeLa Cells; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D020014:K562 Cells; D061986:MCF-7 Cells; D011485:Protein Binding; D011487:Protein Conformation; D011965:Receptors, Glucocorticoid / Q000235:genetics* / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; C506487:ESR1 protein, human; D047628:Estrogen Receptor alpha; C496499:FOXA1 protein, human; D051541:Hepatocyte Nuclear Factor 3-alpha; D011965:Receptors, Glucocorticoid; D012097:Repressor Proteins