RT Journal Article SR Electronic T1 Combinatorial analysis of Saccharomyces cerevisiae regulatory elements JF bioRxiv FD Cold Spring Harbor Laboratory SP 777763 DO 10.1101/777763 A1 N. Dhillon A1 R. Shelansky A1 B. Townshend A1 M. Jain A1 H. Boeger A1 D. Endy A1 R.T. Kamakaka YR 2019 UL http://biorxiv.org/content/early/2019/09/23/777763.abstract AB Gene expression in Saccharomyces cerevisiae is regulated at multiple levels. Genomic and epigenomic mapping of transcription factors and chromatin components has led to the definition and delineation of various regulatory elements. Enhancers, promoters, 5’ untranslated regions (5’UTR) and transcription terminators/3’ untranslated regions (3’UTR) have all been defined. However, the specific contributions of each of these features as part of a regulatory unit and the functional communications between these regulatory elements remains under explored.We built a combinatorial library of 26 different enhancers, core promoters, 5’UTRs and transcription terminators/3’UTRs. This library was analyzed with respect to gene expression in order to better understand the interactions between different regulatory elements. In the process we developed new methods to estimate the contribution of individual regulatory parts from just a few simple measurements. Our data show that different pairs of regulatory parts follow specific interaction rules affecting overall activity either positively or negatively. We find that while enhancers are the initiators of gene activity, core promoters modulate the levels of enhancer mediated expression. Cluster analysis based on expression show that TATA-box containing core promoters appear to increase enhancer-driven transcription to a greater extent than TATA-less promoters. Principal component analysis highlight outliers and suggest differences in mechanisms of regulation. These results provide a system to characterize regulatory elements and use these elements in the design of synthetic regulatory circuits.