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

Abstract

Sister chromatids, the products of eukaryotic DNA replication, are held together by the chromosomal cohesin complex after their synthesis. This allows the spindle in mitosis to recognize pairs of replication products for segregation into opposite directions. Cohesin forms large protein rings that may bind DNA strands by encircling them, but the characterization of cohesin binding to chromosomes in vivo has remained vague. We have performed high resolution analysis of cohesin association along budding yeast chromosomes III-VI. Cohesin localizes almost exclusively between genes that are transcribed in converging directions. We find that active transcription positions cohesin at these sites, not the underlying DNA sequence. Cohesin is initially loaded onto chromosomes at separate places, marked by the Scc2/Scc4 cohesin loading complex, 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 the sites of cohesin binding and therefore probably sister chromatid cohesion, a key architectural feature of mitotic chromosomes, display surprising flexibility. Cohesin localization to places of convergent transcription is conserved in fission yeast, suggesting that it is a common feature of eukaryotic chromosomes.

Figure 1

Cohesin localises to convergent intergene regions along budding yeast chromosome VI. Cells containing Smc3-Flag₃ or Scc1-HA₆ were arrested in metaphase by nocodazole treatment and processed for ChIP against the epitope tagged subunits. Enrichment in the immunoprecipitated fraction relative to a whole genome DNA sample is shown along the length of the chromosome. Each bar represents the average of 16 oligonucleotide probes within adjacent 300 bp windows. The y-axis scale is log₂. Dark grey signals represent significant binding, as detailed in the Supplementary MIAME Document. Blue bars above and below the midline are genes transcribed from left to right and opposite, respectively. The purple oval represents the centromere. Origins of replication are depicted in red, tRNA genes in yellow, and a Ty2 transposon in green.

Figure 2

Cohesin is moved towards 3′-ends of genes by their transcription. a, Localisation of Scc1-HA₆ around STE2 on chromosome VI in a nocodazole-arrested wild-type strain (top), and after deletion of the STE2 promoter (bottom). b, Localisation of Scc1-HA₆ around MSH4, close to centromere VI, in mitotic cells (top), and of Rec8-Flag₃ in meiosis (bottom) when MSH4 is induced. c, Localisation of Scc1-HA₆ in nocodazole-arrested cells before (top) and 15 min after heat-shock (bottom). Regions around HSP30 and SRO9 on chromosome III, induced and repressed after heat-shock respectively, are shown.

Figure 3

Cohesin loading at, and movement away from sites of Scc2/Scc4 binding. a, Localisation of Scc4-HA₆ and Scc2-HA₆ along chromosome VI in hydroxyurea-arrested cells. See the legend to chromosomal features in Fig. 1. b, Transcriptional activity along chromosome VI in wild-type logarithmically growing cells. The signal intensity reflects the abundance of transcripts, as an approximation of transcriptional activity. Broken bars exceed 10,000, see Supplementary Figure S5 for full values c, Detail of the localisation on the left arm of chromosome VI, from top to bottom, of Scc2-HA₆ in hydroxyurea-arrested cells, Scc1-HA₆ in scc2-4 mutant cells released from G1 into hydroxyurea block at restrictive temperature, Scc1-HA₆ in wild-type cells 10 min, and 30 min following release from G1 at 16°C, and Scc1-HA₆ in hydroxyurea-arrested wild-type cells. The green and red dashed lines flank sites usually seen bound by Scc2 and Scc1, respectively.

Figure 4

Cohesin localisation to convergent intergenic regions is conserved in fission yeast. ChIP was performed against the cohesin subunit Rad21-HA₃ from logarithmically growing cells. A 240 kb long stretch from the right arm of chromosome 2 is shown.