Cohesin relocation from sites of chromosomal loading to places of convergent transcription

Abstract

Sister chromatids, the products of eukaryotic DNA replication, are held together after their synthesis by the chromosomal cohesin complex. This allows the spindle in mitosis to recognise pairs of replication products for segregation into opposite direction1-6. Cohesin forms large protein rings that may bind DNA strands by encircling7, but the characterisation of cohesin binding to chromosomes in vivo has remained vague. Here, we present high resolution analysis of cohesin association along budding yeast chromosomes III -VI. Cohesin localises almost exclusively between genes transcribed in converging direction. We find that not the underlying sequence, but active transcription positions cohesin at these sites. Cohesin is initially loaded onto chromosomes at separate places, marked by the Scc2/Scc4 cohesin loading complex8, from where it appears to slide to its more permanent locations. But even after sister chromatid cohesion is established changes in transcription lead to repositioning of cohesin. Thus a key architectural feature of mitotic chromosomes, the sites of cohesin binding and therefore most likely sister chromatid cohesion, display surprising flexibility. Cohesin localisation to places of convergent transcription is conserved in fission yeast, suggesting that it is a common feature of eukaryotic chromosomes.Correspondence and requests for materials should be addressed to F.U. (e-mail: frank.uhlmann@cancer.org.uk).. * these authors contributed equally Supplementary Information accompanies the paper on Nature's website (http://www.nature.com). Cohesin association with yeast and human chromosomes has been studied4,9-15, but the defining characteristics of association sites, and how cohesin gets to these sites, remained unclear. We analysed cohesin binding to chromosome VI of the budding yeast Saccharomyces cerevisiae by chromatin immunoprecipitation (ChIP) followed by hybridisation to a high-density oligonucleotide array16. The pattern of association in metaphase was similar for all cohesin subunits analysed, Scc1, Scc3, Smc3, and Pds5 ( Fig. 1, and Supplementary Figure S1). It was also similar before the establishment of sister chromatid cohesion, in cells arrested with the replication inhibitor hydroxyurea (Ref. 9, and Supplementary Figure S1). Cohesin bound 28 distinct sites, each spanning 1-4 kilobases (kb) in width. The intensity of association varied, with the strongest peaks found around the centromere, consistent with previous analyses9-11. The distance between neighbouring cohesin association sites ranged from 2 to 35 kb. Almost all cohesin association sites were centred in intergenic regions where genes from opposite strands converged (Fig. 1a), as previously suggested17. Using an additional high-density array, we also mapped the association of Scc1 with chromosomes III, IV, and V (Supplementary Table 1 and Figure S2). 91% (276 of 304) cohesin association sites identified lie at intergenic regions between converging genes, and of 328 convergent intergene regions 84% were bound by cohes...

Shugoshin regulates cohesion by driving relocalization of PP2A in Xenopus extracts

“…We favor the first possibility. No report to date has shown that cohesin is enriched at centromeres prior to mitosis in metazoa, although this is the case in yeast (e.g., Lengronne et al 2004). Thus, centromeric cohesin enrichment may be the result of preferential dissociation of cohesin from chromosome arms and protection at centromeres.…”

Functional links between Drosophila Nipped-B and cohesin in somatic and meiotic cells

“…In S. cerevisiae, cohesin does not colocalize with the Scc2 ortholog of Nipped-B on chromosomes (Lengronne et al 2004). Nevertheless, purification of yeast Scc2-Scc4 complex brings along small amounts of cohesin subunits, and thus it has also been proposed that the Scc2-Scc4 complex also directly regulates binding of cohesin to chromosomes (Arumugam et al 2003).…”

“…Nevertheless, purification of yeast Scc2-Scc4 complex brings along small amounts of cohesin subunits, and thus it has also been proposed that the Scc2-Scc4 complex also directly regulates binding of cohesin to chromosomes (Arumugam et al 2003). It is suggested that cohesin loads at Scc2-binding sites and translocates away (Lengronne et al 2004). In contrast, chromatin immunoprecipitation experiments using cultured Drosophila cells reveals that Nipped-B colocalizes with cohesin in the entire nonrepetitive genome, confirming that their colocalization is not unique to polytene and meiotic chromosomes (Misulovin et al, submitted for publication).…”

Cohesin and chromatin organisation

“…Cohesin is largely excluded from repressed regions of the Drosophila genome that are marked by Polycomb protein binding and trimethylation of lysine 27 of histone H3 (H3K27me3) [46]. In stark contrast to Drosophila, yeast cohesin is excluded from actively transcribed genes and instead accumulates between convergently transcribed genes [47,48] [51].…”

“…Cohesin is largely excluded from repressed regions of the Drosophila genome that are marked by Polycomb protein binding and trimethylation of lysine 27 of histone H3 (H3K27me3) [46]. In stark contrast to Drosophila, yeast cohesin is excluded from actively transcribed genes and instead accumulates between convergently transcribed genes [47,48]. In the fission yeast S. Pombe, cohesin even functions as a terminator of RNA polymerase progression, and is recruited to sites of convergent transcription by the RNA interference (RNAi) transcriptional gene-silencing pathway [49].…”