A Sir2-regulated locus control region in the recombination enhancer ofSaccharomyces cerevisiaespecifies chromosome III structure
Authors: Li Mingguang , Fine Ryan D. , Dinda Manikarna , Bekiranov Stefan , Smith Jeffrey S. 
Published: February 2019

The NAD+-dependent histone deacetylase Sir2 was originally identified inSaccharomyces cerevisiaeas a silencing factor forHMLandHMR, the heterochromatic cassettes utilized as donor templates during mating-type switching.MATa cells preferentially switch toMATα usingHMLas the donor, which is driven by an adjacentcis-acting element called the recombination enhancer (RE). In this study we demonstrate that Sir2 and the condensin complex are recruited to the RE exclusively inMATa cells, specifically to the promoter of a small gene within the right half of the RE known asRDT1. We go on to demonstrate that theRDT1promoter functions as a locus control region (LCR) that regulates both transcription and long-range chromatin interactions. Sir2 represses the transcription ofRDT1until it is redistributed to a dsDNA break at the MAT locus induced by the HO endonuclease during mating-type switching. Condensin is also recruited to theRDT1promoter and is displaced upon HO induction, but does not significantly repressRDT1transcription. Instead condensin appears to promote mating-type switching efficiency and donor preference by maintaining proper chromosome III architecture, which is defined by the interaction ofHMLwith the right arm of chromosome III, includingMATa andHMR. Remarkably, eliminating Sir2 and condensin recruitment to theRDT1promoter disrupts this structure and reveals an aberrant interaction betweenMATa andHMR, consistent with the partially defective donor preference for this mutant. Global condensin subunit depletion also impairs mating type switching efficiency and donor preference, suggesting that modulation of chromosome architecture plays a significant role in controlling mating type switching, thus providing a novel model for dissecting condensin functionin vivo.

Author summary

Sir2 is a highly conserved NAD+-dependent protein deacetylase and defining member of the sirtuin protein family. It was identified about 40 years ago in the budding yeast,Saccharomyces cerevisiae, as a gene required for silencing of the cryptic mating-type loci,HMLandHMR. These heterochromatic cassettes are utilized as templates for mating-type switching, whereby a programmed DNA double-strand break at theMATa orMATα locus is repaired by gene conversion to the opposite mating type. The preference for switching to the opposite mating type is called donor preference, and inMATa cells, is driven by a cis-acting DNA element called the recombination enhancer (RE). It was believed that the only role for Sir2 in mating-type switching was silencing HML and HMR. However, in this study we show that Sir2 also regulates expression of a small gene (RDT1) in the RE that is activated during mating-type switching. The promoter of this gene is also bound by the condensin complex, and deleting this region of the RE drastically changes chromosome III structure and alters donor preference. The RE therefore appears to function as a complex locus control region (LCR) that links transcriptional control to chromatin architecture, and thus provides a new model for investigating the underlying mechanistic principles of programmed chromosome architectural dynamics.