Functional transcription regulatory network reconstruction and characterization

The genome of yeast Saccharomyces cerevisiae encodes more than 5,800 genes with well controlled and coordinated expression patterns for normal cellular functions. Control of gene expression occurs primarily at the transcriptional level via transcription factors. In response to various conditions, these regulators bind to promoters of target genes and recruit additional factors and the transcription machinery to activate or repress transcription. However, the genome-wide details of the transcriptional regulatory networks are largely unknown. We first mapped the genome-wide in vivo DNA binding distribution of Heat Shock Factor (HSF), one of the most highly conserved transcriptional regulators in eukaryotes. HSF mediates the response of cells to many stresses including heat shock, but little is known about its full range of biological targets. We used whole genome analyses to identify virtually all of the direct transcriptional targets of yeast HSF. The majority of the identified loci were heat-inducibly bound by HSF. The target genes encode proteins with a broad range of biological functions. This study provides novel insights into the role of HSF in growth, development, disease and aging, and in the complex metabolic reprogramming in cells in response to stress. Together with a recent study using a similar approach, this has provided a view of the potential regulatory network composed of transcription factors and their binding sites. However, it has been implicated that the binding of a transcription factor does not necessarily lead to an expression change. We therefore profiled the transcriptional response of yeast upon the individual deletion of more than 250 transcriptional regulators under normal growth as well as under heat shock for a subset of those. This enabled us to construct a functional transcription network. Solid support of the network was established. Known and novel roles of transcription factors were inferred and quantitatively verified. From the promoter regions of the target gene sets, we discovered many novel sequence motifs in addition to many previously characterized ones. In conclusion, the present study provides important insights for elucidating the specific roles of transcription factors in mediating the responses of the cells under different conditions.