Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus the centric region

Sister chromatid cohesion is mediated by evolutionary conserved chromosomal proteins, termed "cohesins." Using an extension of chromatin immunoprecipitation, we have analyzed the distribution of cohesins Mcd1/Scc1 and Smc1 along yeast chromosome III. Both proteins occur preferentially at the same similar to 23 positions. Sites in a similar to 50 kb region around the centromere give especially intense signals. Prominent centric region binding appears to emerge from a more even distribution, probably by differential loss of cohesins along the chromosome arms. Cohesin binding peaks correspond closely to peaks of high local AT composition, a base composition periodicity of similar to 15 kb that is distinct from the similar to 50 kb periodicity of base composition isochores, consistent with axis association of cohesins. The methodology described can be used to analyze the distribution of any DNA-binding protein and, via microchips, along entire genomes.