Hi, I was reading some articles where CTCF binding sites co-occur with cohesin (RAD21) binding site with 60-80% in any particular cell. I wanted to know what fraction of these binding sites found inside chromatin interacting regions and outside chromatin interacting regions. What I understand from ChIA-PET technique It find the interaction between two chromatin interacting regions which bound to some transcription factor. So I am confused now that this TF found in all chromatin interacting regions or not? Where is the exact positions of this binding sites in the chromatin loop. One end of the loop or another end of the loop or in the middle? Does both end have the same orientation or different orientation of TFBS? This interacting regions occur in promoter regions or enhancer regions or non-coding regions. What is the difference between binding site if occur in promoter, enhancers or non-coding regions? Is there any other technique rather than ChIA-PET which precisely tells the binding sites in chromatin interacting regions. Thanks.
