Outward-oriented sites within clustered CTCF boundaries are key for intraTAD chromatin interactions and gene regulation

CTCF plays an important role in adjusting insulation at TAD boundaries, where clustered CBS (CTCF-binding site) elements are often arranged in a somewhat tandem array with a complex divergent or convergent orientation. Here using cPcdh and HOXD loci as a paradigm, we look into the clustered CTCF TAD boundaries and find that, counterintuitively, outward-oriented CBS elements are crucial for inward enhancer-promoter interactions as well as for gene regulation. Specifically, by combinatorial deletions of a series of putative enhancer elements in vivo or CBS elements in vitro, in conjunction with chromosome conformation capture and RNA-seq analyses, we show that deletions of outward-oriented CBS elements weaken the strength of intraTAD promoter-enhancer interactions and enhancer activation of target genes. Our data highlight the crucial role of outward-oriented CBS elements within the clustered CTCF TAD boundaries and have interesting implications on the organization principles of clustered CTCF sites within TAD boundaries.