GSE29506
Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4
Binding of transcription factors to DNA is a key regulatory step in the control of gene expression.  DNA sequences with high affinity for transcription factors occur more frequently in the genome than instances of genes bound or regulated by these factors.  Although several mechanisms have been identified that influence the specificity of transcriptional regulation, it is not known if these can explain the observed genome-wide pattern of binding or regulation for a given transcription factor.  We used genome-wide approaches to study how trans influences shape the binding and regulatory landscape of Pho4, a budding yeast transcription factor that activates gene expression in response to phosphate limitation.  We find that nucleosomes significantly restrict the sites to which Pho4 binds. At nucleosome-depleted sites, competition between Pho4 and another transcription factor, Cbf1, determines Pho4 occupancy, raising the threshold for transcriptional activation by Pho4 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 the transcription factor Pho2 and Pho4 occurs specifically at genes that are activated.  Combining these experimental observations, we are able to globally predict Pho4 binding and its functionality.  Our study provides insights into the mechanisms of global control by sequence-specific transcription factors. Overall design: ChIP-Seq experiments of Pho4, Pho2 and Cbf1 samples and paired-end nucleosome sequencing in no Pi conditions.