Integrative analysis reveals extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors

Cys2-His2-zinc-finger proteins (C2H2-ZFPs) form the largest class of human transcription factors, yet their potential roles in higher-order genome organization remain poorly defined. To date, only a few C2H2-ZFPs, e.g. CTCF, have been implicated in chromatin organization. Here, we systematically examined the global relationship between C2H2-ZFPs and long-range chromatin interactions (LRIs). By integrating ChIP-seq datasets for 216 C2H2-ZFPs with genome-wide chromatin interaction maps, we find that >40% of human C2H2-ZFPs are significantly enriched at LRI anchors. Depletion of a subset of such C2H2-ZFPs is associated with altered expression of genes linked by the LRIs they occupy. To investigate whether protein-protein interactions (PPIs) contribute to this pattern, we generated a large-scale interactome using affinity purification-mass spectrometry, encompassing 345 C2H2-ZFPs, and LUMIER binary interaction assays for 204 C2H2-ZFPs, revealing extensive connectivity among the family members. Integrative analysis of PPIs, ChIP-seq, and chromatin interaction datasets revealed that interacting C2H2-ZFP pairs are significantly co-enriched at LRIs and frequently localize to the same or opposing loop anchors. Finally, we show that ∼35% of LRI-associated C2H2-ZFP binding sites overlap somatic mutations in cancer genomes. Together, our results reveal a widespread network of C2H2-ZFP interactions at chromatin loop anchors, providing an important resource for understanding chromatin organization.