Why Do Long Zinc Finger Proteins have Short Motifs? A case study of ZFY and CTCF reveals non-independent recognition of tandem zinc finger proteins.

The human genome has more than 800 C2H2 Zinc Finger-containing genes, and many of them are composed of long tandem arrays of zinc fingers. Current Zinc Finger Protein (ZFP) motif prediction models assume longer finger arrays correspond to longer DNA-binding motifs and higher specificity. However, recent experimental efforts to identify ZFP binding sites contradict this assumption with many having short reported motifs. Using Zinc Finger Y (ZFY), which has 13 ZFs, we quantitatively characterize its DNA binding specificity with several complementary methods, including Affinity-seq, HT-SELEX, Spec-seq and fluorescence anisotropy. Besides the previously identified core motif GGCCT recognized by fingers 12-13, we find a novel secondary irregular motif recognized by accessory fingers. Via high-throughput energy measurements and two-color anisotropy, we establish that this secondary motif contributes to binding and recognition in a non-independent manner, increasing overall affinity only in the presence of the core recognition site. Through additional experimental and iterative computational analysis of CTCF and ZNF343, we further establish that this non-independent recognition between core and secondary motifs could be a general mechanism for tandem zinc finger proteins. These results establish that better motif discovery methods that consider the intrinsic properties of tandem zinc fingers including irregular motif structure, variable spacing and non-independent recognition are essential to improve prediction of ZFP recognition, occupancies, and effects on downstream gene expression .