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New paper: The target search mechanism of CTCF is published in Nature Chemical Biology

12/2/2019

 
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Our BioRxiv preprint on CTCF's target search mechanism is now published in Nature Chemical Biology:
  • We show that CTCF exhibits anisotropic diffusion
  • 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

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