Abstract

Zinc finger proteins (ZFPs or ZNFs) constitute the largest family of transcription factors in mammals; however, their regulatory mechanism remains largely elusive. Here we propose COP (C2H2-ZFP occupancy predictor), a deep learning-based heuristic screening tool that integrates DNA sequence with protein primary and secondary features to assess ZFP genomic enrichments. Applying COP to the mouse clustered protocadherin ( cPcdh ) gene locus, we identified dozens of C2H2-ZFPs potentially involved in CTCF-mediated gene regulation with Wiz (widely interspaced zinc finger-containing protein) having the highest number of 12 ZFs. We confirmed Wiz enrichments at all of the CTCF-binding site (CBS) elements across the three Pcdh clusters by Myc-tagging the endogenous Wiz gene. Genetic experiments revealed significant increases of expression levels of the cPcdh genes upon Wiz deletion in both neuronal cells in vitro and in mouse brain in vivo . Finally, integrated ChIP-seq, RNA-seq, and 4C-seq analyses demonstrated that Wiz regulates CTCF/cohesin occupancy and long-range enhancer-promoter contacts in a genomic-distance biased manner. Together, these findings reveal a key role for Wiz in coupling cohesin occupancy to long-range cPcdh regulation and highlight important functions of C2H2-ZFPs in enhancer-promoter interactions. If you uncoiled the DNA inside a single human cell and stretched it out end-to-end, it would measure about two meters (six feet) long. Yet, this entire blueprint must be packed into the cell’s nucleus, which is microscopic—less than one-tenth the width of a human hair. One of the key mechanisms compacting the three-dimensional (3D) genome is called loop extrusion. In this process, protein complexes such as cohesin act like molecular motors that grab distal DNA elements such as enhancers and promoters together, creating loops of chromatin. Specifically, by squeezing the intervening DNA out into a loop, it physically reels the distant enhancer