Current observations/claims for CTCF in insulation potency and chromatin interactionΒΆ

  • Chromatin interactions are possibly formed by convergent CTCF pairs, although there are tandom CTCF pairs. But the chances of a loop with convergent pair is 3 times higher than a tandem pair.

  • In terms of insulation potency, the number of CTCF sites is important, more sites means more insulation power. But these observation is tested using core TAD boundary CTCF sequences.

  • Replacing TAD boundary CTCF sequences with non-TAD boundary CTCF sequences significantly reduced insulation power. And it seems the +/- 20bp flanking sequences of the 19bp CTCF motif is the key. One known motif is the CTCF-upstream motif, which binds to a Znic-Finger protein.

  • Disruption of the CTCF-upstream motif did not affect CTCF binding.

Reference:

  1. [Loop competition and extrusion model predicts CTCF interaction specificity](https://www.nature.com/articles/s41467-021-21368-0)

  2. [Many facades of CTCF unified by its coding for three-dimensional genome architecture](https://www.sciencedirect.com/science/article/pii/S1673852720301284)

  3. [Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation](https://www.nature.com/articles/s41594-020-00539-5?utm_source=other&utm_medium=other&utm_content=null&utm_campaign=JRCN_1_DD01_CN_NatureRJ_article_paid_XMOL)

  4. [CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains](https://www.nature.com/articles/s41588-021-00863-6?proof=t)

code @ github.