The Transcriptional Regulator Ume6 is a Major Driver of Gene Expression during Gametogenesis in Budding Yeast
Early meiotic genes (EMGs) encompass an important subset within the developmental program of gametogenesis. Regulation of EMGs is achieved through the recognition of a common regulatory element in their promoters by the transcription factor Ume6. Proper meiotic execution requires the timely expression of EMGs, which is achieved through the adoption of the meiotic regulator Ime1 by Ume6. While it is known that Ime1's binding to Ume6 promotes EMG expression, the mechanism of EMG activation remains unclear. Two competing models have been proposed: (1) Ime1 converts Ume6 to a coactivator complex, and (2) Ime1 binding targets Ume6 for degradation. Using a combination of tools including meiotic synchronization, temporally controlled protein depletion, protein-protein interaction engineering, and transcriptomics, here we address this conundrum. We identify 160 genes that are directly regulated by Ime1-Ume6, including UME6 itself. Removal of Ume6 shortly before meiotic entry is detrimental to EMG activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger EMG expression and to generate viable gametes in the absence of Ime1. We conclude that Ime1-Ume6 functions as a coactivator complex. While Ume6 is indispensable for EMGs expression, Ime1 primarily serves as an evolutionarily tuned activation domain for Ume6.  Overall design: (Mitotic Depletion)  Gene expression profiling of RNA-seq data from a time series before (t = -30 and 0min) and after Ume6 depletion (TIR; 15, 30, 60, and 120min) compared to undepleted time matched samples (NoTIR). Then, comparing their expression profiles for wild-type UME6 (WT) and a UME6 null (Ume6Del). Three replicates are included for each. (Meiotic Depletion)  Expression profiling of RNA-seq data from a time series comparing effects of Ume6 depletion (TIR) before (t = 0.5 and 2h) and post-IME1 induction (t = 2.5, 3, 4.5, and 6h). Expression profiles for TIR were then compared to time matched samples for a NoTIR control. Three replicates are included for each. (Meiotic Rescue)  Comparative gene expression profiling from RNA-seq data for a time series (t = 0, 2, 4, 6h) of untagged IME1 or sfGFP-tagged IME1 with various UME6 alleles (UME6, UME6-3V5, UME6(T99N)-3V5, and UME6(T99N)-3V5-aGFP). Three replicates are included. (Meiotic Rescue)  Comparative gene expression profiling from RNA-seq data for a time series (t = 0, 2, 4, 6h) of untagged or sfGFP-tagged activation domains (IME1 and B112) in the UME6(T99N)-3V5-aGFP background. Three replicates are included.