Cohesin is required to prevent premature dissociation of sister chromatids after 
DNA replication. Although its role in chromatid cohesion is well established, 
the functional significance of cohesin's association with interphase chromatin 
is not clear. Using a quantitative proteomics approach, we show that the STAG1 
(Scc3/SA1) subunit of cohesin interacts with the CCTC-binding factor CTCF bound 
to the c-myc insulator element. Both allele-specific binding of CTCF and 
Scc3/SA1 at the imprinted IGF2/H19 gene locus and our analyses of human DM1 
alleles containing base substitutions at CTCF-binding motifs indicate that 
cohesin recruitment to chromosomal sites depends on the presence of CTCF. A 
large-scale genomic survey using ChIP-Chip demonstrates that Scc3/SA1 binding 
strongly correlates with the CTCF-binding site distribution in chromosomal arms. 
However, some chromosomal sites interact exclusively with CTCF, whereas others 
interact with Scc3/SA1 only. Furthermore, immunofluorescence microscopy and 
ChIP-Chip experiments demonstrate that CTCF associates with both centromeres and 
chromosomal arms during metaphase. These results link cohesin to gene regulatory 
functions and suggest an essential role for CTCF during sister chromatid 
cohesion. These results have implications for the functional role of cohesin 
subunits in the pathogenesis of Cornelia de Lange syndrome and Roberts 
syndromes.