Interpreting Hi-C results

[netpumber]

Hi.

I'm reading this paper (doi:10.1038/nature13415) and i'm trying to interpret some data from that plot



Please correct me if i'm wrong.

After a Hi-C experiment they found some sites (boundaries sites) where one place of the chromosome interacts with another (and possibly creates loops).

Below the boundaries sites there is a list of some regulation proteins like CTCF and histones like H3K27me3.

So if there is such a question :
"Is the CTCF insulator protein demarcating boundaries between 3D or chromatin domains?"
could the answer be :
"CTCF protein isn't demarcating boundaries between neither 3D (Hi-C) nor chromatin domains because it seems that it doesn't bind only at the boundaries sites but in a much more sites within the chromosome"
?

[dpryan]

A better answer would be, "The presence of CTCF does not necessarily indicate the presence of a TAD boundary." CTCF has a bunch of functions, only one of which seems to be related to TADS. Further, it seems that the orientation of two CTCF sites relative to each other is important for whether they can be involved in TAD formation.

[netpumber]

Thank you for your answer but how did you make the conclusion on the orientation of the sites ? Where is that info in this graph ?

[dpryan]

CTCF orientation isn't in that plot, it's something described elsewhere in the literature.