Linking Yeast Transcription Factor Structural Class and Detailed Binding Preferences with in vivo Regulatory Functions

Abstract

Cellular responses to internal and external stimuli through changes in gene expression are in part controlled by the binding of regulatory transcription factors (TFs) to specific sequences of DNA. These TFs belong to a wide variety of DNA binding domain (DBD) structural classes. Sequence specificity is diverse between structural classes, but TFs within each class often have apparently redundant sequence preferences. To understand how cells use these regulators to coordinate networks of responses, it is essential to determine how regulatory function is shared and partitioned between factors of similar and different structures and DNA binding specificities. Are certain structural classes better suited for certain functions? Are detailed differences in binding preferences among apparently similar TFs relevant to in vivo function? Using genome-wide datasets, we have described trends in biological function and regulatory mechanisms within TF structural classes in the yeast Saccharomyces cerevisiae. These trends suggest general ways in which TF function may be distributed across structural classes according to the biophysical constraints dictated by each DBD structure. Such analyses do not show, however, how specific details of an individual TF's binding specificity might affect its biological function. New data from protein binding microarrays (PBMs) provide such detailed TF binding preference information at all possible 8 base-pair DNA sequences. By combining these PBM data with in vivo binding locations measured by chromatin immunoprecipitation (ChIP-chip) experiments, we can infer the functional importance of specific types of TF binding sites (ie low and high affinity sites). This and other analyses made possible by the high resolution PBM data, when combined with observed functional trends in structural classes, will demonstrate how the cell utilizes both general and specific biophysical TF properties to accomplish cellular functions.