The yeast Sfp1 protein regulates both cell division and growth but how it coordinates these processes is poorly understood. We demonstrate that Sfp1 directly controls genes required for ribosome production and many other growth-promoting processes. Remarkably, the complete set of Sfp1 target genes is revealed only by a combination of ChIP (chromatin immunoprecipitation) and ChEC (chromatin endogenous cleavage) methods, which uncover two promoter binding modes, one requiring a cofactor and the other a DNA-recognition motif. Glucose-regulated Sfp1 binding at cell cycle "START" genes suggests that Sfp1 controls cell size by coordinating expression of genes implicated in mass accumulation and cell division.
16Understanding how transcriptional programs help to coordinate cell growth and division is an 17 important unresolved problem. Here we report that the nutrient-and stress-regulated transcription 18 factor Sfp1 is rate-limiting for expression of several large classes of genes involved in yeast cell growth, 19 including ribosomal protein, ribosome biogenesis, and snoRNA genes. Remarkably, the spectrum of 20 Sfp1 transcription effects is concordant with a combination of chromatin immunoprecipitation and 21 chromatin endogenous cleavage binding analyses, which together provide evidence for two distinct 22 modes of Sfp1 promoter binding, one requiring a co-factor and the other a specific DNA-recognition 23 motif. In addition to growth-related genes, Sfp1 binds to and regulates the promoters of cell cycle 24 "START" regulon genes, including the key G1/S cyclins CLN1 and CLN2. Our findings suggest that Sfp1 25 acts as a master regulator of cell growth and cell size by coordinating the expression of genes implicated 26 in mass accumulation and cell division. 2728 48 large-cell phenotype (Jorgensen et al., 2002). Taken together, these findings suggest that Sfp1 might 49 play a key role in coordinating cell growth and cell division. Interestingly, the transcriptional and cell-50 size phenotypes of SFP1 are notably similar to those of the c-Myc proto-oncogene (Jorgensen et al.,One paradox that has limited our understanding of Sfp1's mechanism of action is that the protein has 53 been detected by Chromatin Immuno-Precipitation (ChIP) at only a small fraction of the promoters that 54 it appears to regulate. For example, although ChIP detects Sfp1 at many RP gene promoters (Reja, 55 Vinayachandran et al., 2015), it is undetectable at virtually all of the >200 RiBi gene promoters where 56 4 over-expression studies suggest that it might be a direct activator (Jorgensen et al., 2002, Jorgensen et 57 al., 2004. 58Here we vastly expand our knowledge of Sfp1 binding by Chromatin Endogenous Cleavage (ChEC)-seq 59 analysis (Schmid, Durussel et al., 2004, Zentner, Kasinathan et al., 2015. Remarkably, we find that 60 ChEC and ChIP provide a highly complementary picture of Sfp1 binding, with distinct sets of sites 61 identified by one technique or the other. Our combined analysis provides evidence that Sfp1 directly 62 orchestrates TATA-binding protein (TBP) and RNAPII recruitment at a broad array of genes that drive 63 cell growth, including most RiBi, RP and snoRNA genes. In addition, we find that Sfp1 binds to the 64 promoters of many G1/S ("START") regulon genes that are targeted by the TF Swi4. Interestingly, Sfp1 65 binding sites identified by ChEC are enriched for the motif gAAAATTTTc, whereas binding identified by 66 ChIP is often strongly dependent on another TF: Ifh1 at RP genes or Swi4 at G1/S regulon genes. These 67 findings provide an unprecedented example of how the combination of ChIP and ChEC can reveal a 68 more complete picture of TF-chromatin interactions. Taken together, our results support a role for 69 Sfp1 as ...
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