The 3-dimensional (3D) structure of the genome compartmentalises chromatin into Topologically Associating Domains (TADs) and demarcates regions of activity and repression. 3D chromatin interactions can be cell type specific or constitutive and together facilitate contacts between promoters and regulatory elements to regulate gene expression. The architectural protein CTCF is a mediator of chromatin conformation, however results of CTCF knockdown experiments do not demonstrate a clear relationship between loss of CTCF, change in chromatin conformation and the epigenome and alteration to gene expression. To characterise mechanisms of CTCF function we performed RNAi knockdown to deplete CTCF and investigate the effect on RNA expression and chromatin architecture. CTCF ChIP-seq following knockdown revealed that ~11% of CTCF-bound sites were robustly resistant to protein depletion. Notably, we found that resistant CTCF sites were enriched at TAD boundaries and at chromatin interactions constitutive to all cell types. In line with this result, TAD boundaries with resistant CTCF sites were enriched for housekeeping genes. Deletion by CRISPR-Cas9 of 2 resistant CTCF sites at the boundary of a long-range active and repressed region within the Kallikrein (KLK) locus resulted in the concordant activation of all 8 KLK genes within the repressive region. HiC demonstrated that genome-wide depletion of CTCF resulted in merging of some TADs. Interestingly we found that the persistent CTCF sites were located at the boundaries of the larger TADs. Together our data demonstrates that there is a subset of CTCF sites, that are involved in cell-type constitutive higher order chromatin architecture and modulation of these sites can cause localised changes to gene expression.