title: NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class.
abstract: ChIP-seq experiments detect the chromatin occupancy of known transcription factors in a genome-wide fashion. The comparisons of several species-specific ChIP-seq libraries done for different transcription factors have revealed a complex combinatorial and context-specific co-localization behavior for the identified binding regions. In this study we have investigated human derived ChIP-seq data to identify common cis-regulatory principles for the human transcription factor c-Fos. We found that in four different cell lines, c-Fos targeted proximal and distal genomic intervals show prevalences for either AP-1 motifs or CCAAT boxes as known binding motifs for the transcription factor NF-Y, and thereby act in a mutually exclusive manner. For proximal regions of co-localized c-Fos and NF-YB binding, we gathered evidence that a characteristic configuration of repeating CCAAT motifs may be responsible for attracting c-Fos, probably provided by a nearby AP-1 bound enhancer. Our results suggest a novel regulatory function of NF-Y in gene-proximal regions. Specific CCAAT dimer repeats bound by the transcription factor NF-Y define this novel cis-regulatory module. Based on this behavior we propose a new enhancer promoter interaction model based on AP-1 motif defined enhancers which interact with CCAAT-box characterized promoter regions.
authors: Institute of Bioinformatics, University Medical Center Göttingen (UMG), Georg-August-University Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
authors: Martin
authors: M
authors: Haubrock
authors: Institute of Bioinformatics, University Medical Center Göttingen (UMG), Georg-August-University Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
authors: Fabian
authors: F
authors: Hartmann
authors: Institute of Bioinformatics, University Medical Center Göttingen (UMG), Georg-August-University Göttingen, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
authors: Edgar
authors: E
authors: Wingender
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D023081:CCAAT-Binding Factor / Q000737:chemistry* / Q000378:metabolism*; D045744:Cell Line, Tumor; D019281:Dimerization; D006801:Humans; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D016760:Proto-Oncogene Proteins c-fos / Q000737:chemistry / Q000378:metabolism*; D018808:Transcription Factor AP-1 / Q000378:metabolism; D050880:p300-CBP Transcription Factors / Q000378:metabolism
chemical_list: D023081:CCAAT-Binding Factor; D016760:Proto-Oncogene Proteins c-fos; D018808:Transcription Factor AP-1; D050880:p300-CBP Transcription Factors