We devise the Anisotropic Diffusion through transient Trapping in Zones model (ADTZ-model) to theoretically explain the data
We show that the zones likely correspond to CTCF clusters
Deleting the internal RNA-Binding Region (RBRi) in CTCF strongly reduces both trapping and CTCF clustering
Our results suggest two sources of CTCF anisotropy: DNA-mediated interactions that causes anisotropy without a defined scale and RNA-mediated interactions which result in local trapping
Functionally, transient RBRi-mediated trapping serves to accelerate the cognate DNA-target search. The presence of the RBRi-domain does not affect DNA-binding, but increases the rate at which CTCF finds a cognate DNA target site by ~2.5-fold!!!.
Thus, the DNA-target search mechanism of CTCF appears to be 'guided' by RNA