ArticleNucleic acids research2015
A systematic survey of the Cys2His2 zinc finger DNA-binding landscape.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
- OsIDD7 integrates signaling networks for arbuscular mycorrhizal symbiosis.Nature communications · 2026Article
- Incorporating AI-optimized zinc finger proteins enhances the efficiencies and targeting ranges of miniature base editors.Nature communications · 2026Article
- Expanding the phenotypic spectrum associated with ZIC1 variants: A neurodevelopmental disorder with and without craniosynostosis.Genetics in medicine : official journal of the American College of Medical Genetics · 2026Article
- The Structure, Classification, Functional Diversity and Regulatory Mechanism of Plant C2H2 Transcription Factors.Biology · 2026Review
- The evolutionary entanglement of flipons with zinc fingers and retroelements has engendered a large family of Z-DNA and G-quadruplex binding proteins.Open biology · 2025Article
- Machine-guided dual-objective protein engineering for deimmunization and therapeutic functions.Cell systems · 2025Article
- Structural insights into a highly flexible zinc finger module unravel INSM1 function in transcription regulation.Nature communications · 2025Article
- DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders.American journal of human genetics · 2025Article
- A transcription network underlies the dual genomic coordination of mitochondrial biogenesis.eLife · 2024Article
- Activation of recombinases at specific DNA loci by zinc-finger domain insertions.Nature biotechnology · 2024Article
- A transcription network underlies the dual genomic coordination of mitochondrial biogenesis.bioRxiv : the preprint server for biology · 2024Article
- Improving prediction performance of general protein language model by domain-adaptive pretraining on DNA-binding protein.Nature communications · 2024Article
- Modulating Mitochondrial DNA Heteroplasmy with Mitochondrially Targeted Endonucleases.Annals of biomedical engineering · 2024Review
- Geometric deep learning of protein-DNA binding specificity.Nature methods · 2024Article
- Updated understanding of the protein-DNA recognition code used by C2H2 zinc finger proteins.Current opinion in structural biology · 2024Review
- New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity.Nucleic acids research · 2024Article
- SETDB1 deletion causes DNA demethylation and upregulation of multiple zinc-finger genes.Molecular biology reports · 2024Article
- Keep Fingers on the CpG Islands.Epigenomes · 2024Article
- Article
- Structures of CTCF-DNA complexes including all 11 zinc fingers.Nucleic acids research · 2023Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
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.
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