A putative condensin loading factor that controls yeast chromosome III architecture

Condensin plays an important and evolutionarily conserved role in mitotic chromosome condensation, three-dimensional genome organization and regulation of gene expression. Condensin is a multi-subunit complex that has natural affinity for the promoters of highly transcribed genes, and also associates with specific transcription factors. However, a general mechanism for functional loading of the complex onto chromatin remains elusive. Our lab previously demonstrated that in haploid MATa yeast cells, condensin and Sir2 (a histone deacetylase) both associate with the recombination enhancer (RE), a cis-acting element on chromosome III that directs donor preference of mating-type switching. Here, Sir2 locally regulates transcription of a small gene called RDT1, while condensin contributes to the 3-dimensional organization of chromosome III, as well as donor preference, indicating that the RDT1 promoter region acts as a locus control region (Li et al., 2019). We have now further characterized the mechanism of condensin recruitment to the RDT1 promoter LCR, and uncovered a critical role for a non-meiotic version of the monopolin complex, known as cohibin (Lrs4 and Csm1 subunits), analogous to its known role in recruiting condensin to the rDNA locus. To test if cohibin functions more generally in condensin loading, or as a condensin accessory factor, we have performed ChIP-seq for genome-wide condensin binding sites in WT and lrs4∆ strains. Numerous Brn1 peaks (including RDT1 and the rDNA) were eliminated or significantly reduced by lrs4∆, consistent with the condensin loader hypothesis. Micro-C XL was then used to characterize the general effects of defective condensin recruitment on genomic conformation in a lrs4∆ mutant, or when the Brn1 condensin subunit was depleted using an auxin-inducible degron system. Alterations were observed on multiple chromosomes, though the most severe changes occurred on chromosome III, which had significant negative effects on the efficiency of mating-type switching, as well as donor preference. We therefore hypothesize that cohibin (Lrs4/Csm1) is indeed a condensin loader at the RDT1 promoter region, where it establishes chromosome III conformation, potentially through a loop extrusion mechanism. Evidence for direct recruitment of condensin by the cohibin complex at other genomic sites and any possible role for cohibin in chromosome condensation are currently under investigation.