Chl1 DNA helicase and Scc2 function in chromosome condensation through cohesin deposition

Abstract

Chl1 DNA helicase promotes sister chromatid cohesion and associates with both the cohesion establishment acetyltransferase Eco1/Ctf7 and the DNA polymerase processivity factor PCNA that supports Eco1/Ctf7 function. Mutation in CHL1 results in precocious sister chromatid separation and cell aneuploidy, defects that arise through reduced levels of chromatin-bound cohesins which normally tether together sister chromatids (trans tethering). Mutation of Chl1 family members (BACH1/BRIP/FANCJ and DDX11/ChlR1) also exhibit genotoxic sensitivities, consistent with a role for Chl1 in trans tethering which is required for efficient DNA repair. Chl1 promotes the recruitment of Scc2 to DNA which is required for cohesin deposition onto DNA. There is limited evidence, however, that Scc2 also directs the deposition onto DNA of condensins which promote tethering in cis (intramolecular DNA links). Here, we test the ability of Chl1 to promote cis tethering and the role of both Chl1 and Scc2 to promote condensin recruitment to DNA. The results reveal that chl1 mutant cells exhibit significant condensation defects both within the rDNA locus and genome-wide. Importantly, chl1 mutant cell condensation defects do not result from reduced chromatin binding of condensin, but instead through reduced chromatin binding of cohesin. We tested scc2-4 mutant cells and similarly found no evidence of reduced condensin recruitment to chromatin. Consistent with a role for Scc2 specifically in cohesin deposition, scc2-4 mutant cell condensation defects are irreversible. We thus term Chl1 a novel regulator of both chromatin condensation and sister chromatid cohesion through cohesin-based mechanisms. These results reveal an exciting interface between DNA structure and the highly conserved cohesin complex.

Promotion of hyperthermic-induced rDNA hypercondensation inSaccharomyces cerevisiae

“…While there is a paucity of evidence that physically links Eco1 to Hsp82, it remains formally possible that Hsp82 promotes rDNA hypercondensation through Eco1 acetylation of cohesin subunits. In contrast to reports that Hsp82 promotes sister chromatid cohesion through stabilization of Chl1 DNA helicase (Khurana et al, 2018), which in turn promotes both Scc2 and cohesin binding to DNA (Skibbens, 2004; Rudra and Skibbens, 2012; Shen and Skibbens, 2017b; Mayer et al, 2004; Xu et al, 2007; Borges et al, 2013; Samora et al, 2016), we find no evidence in the current study that Chl1 (or changes in cohesin/condensin dynamics) adversely impacts rDNA hypercondensation. Future studies will be required to ascertain the extent to which, histone, cohesin and/or condensin modifications promote hyperthermic-induced rDNA hypercondensation in an Hsp90-dependent manner (Figure 7).…”

“…Importantly, rDNA in scc2-4 mutant cells fully hypercondense into very short loops after incubation at 37°C for 1 hour (Figure 1B, C). We confirmed that this scc2-4 mutant strain is indeed temperature sensitive and defective in cohesin deposition onto chromatin (Shen and Skibbens, 2017b). Thus, temperature-induced rDNA hypercondensation during mitosis occurs in the absence of de novo cohesin deposition.…”

“…In contrast, cohesin inactivation quickly results in rDNA puff structures and cohesion loss (Guacci et al, 1994; Guacci et al, 1997; D’Ambrosio et al, 2008; Lopez-Serra et al, 2013; Tong and Skibbens, 2015; Lavoie et al, 2002; Lavoie et al, 2004; Shen and Skibbens, 2017a). We further note that thermic-induced hypercondensation appears to effect rDNA specifically (Shen and Skibbens, 2017a), while cohesins and condensin impact chromatin architecture genome-wide (Shen and Skibbens, 2017b; Rudra and Skibbens, 2012; Skibbens, 2004; Mayer et al, 2004; Xu et al, 2007; Borges et al, 2013; Samora et al, 2016). Importantly, potent Hsp90 ATP-binding/hydrolysis inhibitors Geldanamycin and Radicicol (Chen et al, 2012; Wider et al, 2009; Theodoraki et al, 2012; Millson et al, 2014; Roe et al, 1999) both failed to adversely impact hyperthermic-induced rDNA (current study).…”

“…As expected, mitotic wildtype cells maintained at 23°C contained long rDNA loops while the rDNA of mitotic cells shifted to 37°C during the final hour of incubation hypercondensed into very short loops (Figure 1B), consistent with prior findings (Shen and Skibbens, 2017a; Matos-Perdomo and Machín, 2018a). Prior analyses of these cells revealed that only a fraction of scc2-4 mutant cells contain condensed rDNA loci at 23°C, a level which is retained after shifting to 37°C during the final hour of incubation (Shen and Skibbens, 2017b). We thus limited our current measurements to the fraction of cells in which rDNA loops were tightly cohered and condensed into discrete loops (Figure 1B).…”

“…Chl1 DNA helicase is a positive regulator of both sister chromatid cohesion and chromosome condensation in that Chl1 promotes both Scc2 and cohesin binding to DNA (Skibbens, 2004; Mayer et al, 2004; Inoue et al, 2007; Xu et al, 2007; Laha et al, 2011; Rudra and Skibbens, 2012; Borges et al, 2013; Samora et al, 2016; Shen and Skibbens, 2017b), providing a further opportunity to assess whether cohesin deposition/release are involved in hyperthermic-induced rDNA hypercondensation. We previously reported analyses of rDNA loop lengths in wildtype cells (adapted from Figure 1E in Shen and Skibbens, 2017a), but at that time did not include quantification of rDNA loop lengths in chl1 mutant cells that were simultaneously assessed.…”