ccctc binding factor ctcf is an architectural protein involved in the three dimensional 3d organization of chromatin in this study we assayed the 3d genomic contact profiles of a large number of ctcf binding sites with high resolution 4c seq as recently reported our data also suggest that chromatin loops preferentially form between ctcf binding sites oriented in a convergent manner to directly test this we used crispr cas9 genome editing to delete core ctcf binding sites in three loci including the ctcf site in the sox2 super enhancer in all instances ctcf and cohesin recruitment were lost and chromatin loops with distal convergent ctcf sites were disrupted or destabilized re insertion of oppositely oriented ctcf recognition sequences restored ctcf and cohesin recruitment but did not re establish chromatin loops we conclude that ctcf binding polarity plays a functional role in the formation of higher order chromatin structure.