title: A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.
abstract: Cys2His2 zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding domains. Despite this domain's well-defined DNA-recognition interface, and its successful use in the design of chimeric proteins capable of targeting genomic regions of interest, much remains unknown about its DNA-binding landscape. To help bridge this gap in fundamental knowledge and to provide a resource for design-oriented applications, we screened large synthetic protein libraries to select binding C2H2-ZF domains for each possible three base pair target. The resulting data consist of >160 000 unique domain-DNA interactions and comprise the most comprehensive investigation of C2H2-ZF DNA-binding interactions to date. An integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains and led to the successful design and prediction of C2H2-ZF DNA-binding specificities. Computational analyses uncovered important aspects of C2H2-ZF domain-DNA interactions, including the roles of within-finger context and domain position on base recognition. We observed the existence of numerous distinct binding strategies for each possible three base pair target and an apparent balance between affinity and specificity of binding. In sum, our comprehensive data help elucidate the complex binding landscape of C2H2-ZF domains and provide a foundation for efforts to determine, predict and engineer their DNA-binding specificities.
authors.affiliation: The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Anton V
authors.initials: AV
authors.lastname: Persikov
authors.affiliation: The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Joshua L
authors.initials: JL
authors.lastname: Wetzel
authors.affiliation: The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Elizabeth F
authors.initials: EF
authors.lastname: Rowland
authors.affiliation: The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Benjamin L
authors.initials: BL
authors.lastname: Oakes
authors.affiliation: The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Denise J
authors.initials: DJ
authors.lastname: Xu
authors.affiliation: The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA Department of Computer Science, Princeton University, Princeton, NJ 08544, USA mona@cs.princeton.edu.
authors.forename: Mona
authors.initials: M
authors.lastname: Singh
authors.affiliation: The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA mnoyes@princeton.edu.
authors.forename: Marcus B
authors.initials: MB
authors.lastname: Noyes
mesh_terms: D001665:Binding Sites; D003545:Cysteine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D003625:Data Collection; D006639:Histidine / Q000737:chemistry*; D016335:Zinc Fingers
chemical_list: D006639:Histidine; D004247:DNA; D003545:Cysteine