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CTCF does not generally bind enhancers and promoters, so the authors searched for proteins that could bind to these elements and facilitate their interaction. They identified another zinc
finger protein, YY1, which, like CTCF, is essential for cell viability and is ubiquitously expressed. Importantly, co-immunoprecipitation of differentially tagged YY1 proteins confirmed that
YY1 can form homodimers.
In various mouse and human cell types, YY1 occupied enhancers and promoters genome-wide. As expected from the cell-type specificity of enhancer function, YY1 enhancer occupancy tended to be
cell-type specific. Using methods such as HiChIP, which combine chromatin immunoprecipitation with chromosome conformation capture, the authors showed that YY1 mainly associated with
enhancer–promoter interactions, including more complex contacts between super-enhancer elements and their target promoters. By contrast, the majority of CTCF-associated interactions
connected insulator elements, in agreement with their role in forming TADs.
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