title: Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4.
abstract: DNA sequences with high affinity for transcription factors occur more frequently in the genome than instances of genes bound or regulated by these factors. It is not clear what factors determine the genome-wide pattern of binding or regulation for a given transcription factor. We used an integrated approach to study how trans influences shape the binding and regulatory landscape of Pho4, a budding yeast transcription factor activated in response to phosphate limitation. We find that nucleosomes significantly restrict Pho4 binding. At nucleosome-depleted sites, competition from another transcription factor, Cbf1, determines Pho4 occupancy, raising the threshold for transcriptional activation in phosphate replete conditions and preventing Pho4 activation of genes outside the phosphate regulon during phosphate starvation. Pho4 binding is not sufficient for transcriptional activation-a cooperative interaction between Pho2 and Pho4 specifies genes that are activated. Combining these experimental observations, we are able to globally predict Pho4 binding and its functionality.
authors.affiliation: Howard Hughes Medical Institute, Harvard University Faculty of Arts and Sciences Center for Systems Biology, Northwest Labs, 52 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Xu
authors.initials: X
authors.lastname: Zhou
authors.forename: Erin K
authors.initials: EK
authors.lastname: O'Shea
mesh_terms: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000378:metabolism; D001665:Binding Sites; D001667:Binding, Competitive; D002843:Chromatin / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D018398:Homeodomain Proteins / Q000378:metabolism; D009707:Nucleosomes; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; C064042:CBF1 protein, S cerevisiae; D002843:Chromatin; D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D009707:Nucleosomes; C051611:PHO2 protein, S cerevisiae; C060292:PHO4 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors