A Sir2-regulated locus control region in the recombination enhancer ofSaccharomyces cerevisiaespecifies chromosome III structure

Abstract

22The NAD + -dependent histone deacetylase Sir2 was originally identified in Saccharomyces 23 cerevisiae as a silencing factor for HML and HMR, the heterochromatic cassettes utilized as 24 donor templates during mating-type switching. MATa cells preferentially switch to MATa using 25 HML as the donor, which is driven by an adjacent cis-acting element called the recombination 26 enhancer (RE). In this study we demonstrate that Sir2 and the condensin complex are recruited to 27 the RE exclusively in MATa cells, specifically to the promoter of a small gene within the right 28 half of the RE known as RDT1. We go on to demonstrate that the RDT1 promoter functions as a 29 locus control region (LCR) that regulates both transcription and long-range chromatin 30interactions. Sir2 represses the transcription of RDT1 until it is redistributed to a dsDNA break at 31 the MAT locus induced by the HO endonuclease during mating-type switching. Condensin is 32 also recruited to the RDT1 promoter and is displaced upon HO induction, but does not 33 significantly repress RDT1 transcription. Instead condensin appears to promote mating-type 34 switching efficiency and donor preference by maintaining proper chromosome III architecture, 35 which is defined by the interaction of HML with the right arm of chromosome III, including 36MATa and HMR. Remarkably, eliminating Sir2 and condensin recruitment to the RDT1 promoter 37 disrupts this structure and reveals an aberrant interaction between MATa and HMR, consistent 38 with the partially defective donor preference for this mutant. Global condensin subunit depletion 39 also impairs mating type switching efficiency and donor preference, suggesting that modulation 40 of chromosome architecture plays a significant role in controlling mating type switching, thus 41 providing a novel model for dissecting condensin function in vivo. 42 43 3 Author summary 44 Sir2 is a highly conserved NAD + -dependent protein deacetylase and defining member of the 45 sirtuin protein family. It was identified about 40 years ago in the budding yeast, Saccharomyces 46 cerevisiae, as a gene required for silencing of the cryptic mating-type loci, HML and HMR. 47These heterochromatic cassettes are utilized as templates for mating-type switching, whereby a 48 programmed DNA double-strand break at the MATa or MATa locus is repaired by gene 49 conversion to the opposite mating type. The preference for switching to the opposite mating type 50 is called donor preference, and in MATa cells, is driven by a cis-acting DNA element called the 51 recombination enhancer (RE). It was believed that the only role for Sir2 in mating-type 52 switching was silencing HML and HMR. However, in this study we show that Sir2 also regulates 53 expression of a small gene (RDT1) in the RE that is activated during mating-type switching. The 54 promoter of this gene is also bound by the condensin complex, and deleting this region of the RE 55 drastically changes chromosome III structure and alters donor preference. The RE therefore 56 appears ...

Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome

“…NHEJ) keeps the same efficiency along the chromosome. In eukaryotes [64][65][66], recent studies emphasize the importance of the modulation of chromosomal architecture in the control of recombination. Interestingly, the Streptomyces terminal regions form specific chromatin domains in configuration chromosome capture (3C) and show a loose structuration compared to the rest of the chromosome (P. Leblond, M. Marbouty and R. Koszul, personal communication).…”

Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III

“…A third major condensin recruitment site in S. cerevisiae is the recombination enhancer (RE) located adjacent to HML on the left arm of chromosome III (chrIII) (Li et al, 2019; Wu and Haber, 1996). The other silent mating-type locus, HMR , is located on the right arm of chrIII.…”

“…In haploid MAT a cells only (Li et al , 2019), condensin binds to a segment of the RE (the right half) that increases the frequency of HML contacting the right arm of chrIII, including the MAT a locus (Belton et al, 2015; Li et al , 2019). While not required (Szeto et al, 1997; Wu and Haber, 1996), this segment of the RE and its resulting structural contribution instead augment donor preference of mating-type switching in MAT a cells (Li et al , 2019), whereby HML is primarily utilized as the homologous donor template in repairing the DNA double-strand break induced by HO endonuclease at MAT a, thus converting it to MAT α (Haber, 2012). Once cells are switched to MAT α, condensin association with the RE is permanently lost (Li et al , 2019), consistent with the extreme chrIII conformational differences between MAT a and MAT α cells.…”

Statistical mechanics of chromosomes:in vivoandin silicoapproaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and chromatin substrate properties

“…This leads to an ∼7-fold compaction of the DNA chain. The histone octamer is a highly stable unit, composed of two nearly symmetrical halves ( 1 ). The histones are known to be dynamic during transcription in a manner dependent on RNA polymerase II ( 2–10 ).…”