Chromosomal addresses of the cohesin component Mcd1p

We identified the chromosomal addresses of a cohesin subunit, Mcd1p, in viv o by chromatin immunoprecipitation coupled with high resolution PCR-based c hromosomal walking. The mapping of new Mcd1p-binding sites (cohesin-associa ted regions [CARs]) in single-copy sequences of several chromosomes establi sh their spacing (Ng kb), their sequestration to intergenic regions, and th eir association with AT-rich sequences as general genomic properties of CAR s. We show that cohesins are not excluded from telomere proximal regions, a nd the enrichment of cohesins at the centromere at mitosis reflects de novo loading. The average size of a CAR is 0.8-1.0 kb. They lie at the boundari es of transcriptionally silenced regions, suggesting they play a direct rol e in defining the silent chromatin domain. Finally, we identify CARs in tan dem (rDNA) and interspersed repetitive DNA (Ty2 and subtelomeric repeats). Each 9-kb rDNA repeat has a single CAR proximal to the 5S gene. Thus, the p eriodicity of CARs in single-copy regions and the rDNA repeats is conserved . The presence and spacing of CARs in repetitive DNA has important implicat ions for genomic stability and chromosome packaging/condensation.