CCB Seminar: “A systematic approach for predicting DNA recognition byCys2His2 zinc finger proteins” (Anton Persikov, Ph.D.)

Speaker: Anton Persikov, Ph.D., Associate Research Scholar, Princeton University

Topic: A systematic approach for predicting DNA recognition byCys2His2 zinc finger proteins

Cys2His2 zinc finger (ZF) proteins represent the largest class of metazoan DNA-binding domains. Despite the apparent simplicity of their modular recognition interface, much remains unknown about the affinity and specificity of DNA binding. We present a systematic approach to understanding the DNA-binding preferences of ZF proteins. First, we built a high-quality literature-derived experimental database of ZF-DNA binding examples. We performed a detailed analysis of structural and experimental binding data to expand the canonical ZF model by including three additional contacts. We showed that computational approaches including these additional contacts improve predictions of DNA targets of ZF proteins. We analyzed the evolution of the ZF transcription factors across Drosophila species and uncovered that DNA-binding residues tend to be conserved across phylogenetic clades and evolve slower than other diverging residues. For better understanding of the basic mechanisms of DNA recognition, we screened large synthetic protein libraries to select binding ZF domains for each possible three base pair target. The integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains. We observed the existence of numerous distinct binding strategies for each possible DNA target and an apparent balance between affinity and specificity of binding. In sum, our systematic study helped to unravel the complex binding landscape of ZFdomains and provided a foundation for predicting and designing ZF proteins with desired DNA-binding specificities.