ArticleNucleic acids research2014
An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Article
- Updated understanding of the protein-DNA recognition code used by C2H2 zinc finger proteins.Current opinion in structural biology · 2024Review
- Identification of the New GmJAG1 Transcription Factor Binding Motifs Using DAP-Seq.Plants (Basel, Switzerland) · 2024Article
- Neuroepigenetic Editing.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Two zinc finger proteins, VdZFP1 and VdZFP2, interact with VdCmr1 to promote melanized microsclerotia development and stress tolerance in Verticillium dahliae.BMC biology · 2023Article
- Two Sweet Sorghum (International journal of molecular sciences · 2023Article
- Finding motifs using DNA images derived from sparse representations.Bioinformatics (Oxford, England) · 2023Article
- Structural basis for interaction between CLAMP and MSL2 proteins involved in the specific recruitment of the dosage compensation complex in Drosophila.Nucleic acids research · 2022Article
- A deterministic code for transcription factor-DNA recognition through computation of binding interfaces.NAR genomics and bioinformatics · 2022Article
- Genome-editing approaches and applications: a brief review on CRISPR technology and its role in cancer.3 Biotech · 2021Review
- A heterochromatin inducing protein differentially recognizes self versus foreign genomes.PLoS pathogens · 2021Article
- Epigenome engineering: new technologies for precision medicine.Nucleic acids research · 2020Article
- On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF.NAR genomics and bioinformatics · 2020Article
- The geometric influence on the Cys2His2 zinc finger domain and functional plasticity.Nucleic acids research · 2020Article
- Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA.PLoS computational biology · 2020Article
- Deficient histone H3 propionylation by BRPF1-KAT6 complexes in neurodevelopmental disorders and cancer.Science advances · 2020Article
- C2H2 Zinc Finger Proteins: Master Regulators of Abiotic Stress Responses in Plants.Frontiers in plant science · 2020Review
- Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the λ Cro complex.Nucleic acids research · 2019Article
- Similarity regression predicts evolution of transcription factor sequence specificity.Nature genetics · 2019Article
- Article
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14 authors.
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Abstract
Cys(2)-His(2) zinc finger proteins (ZFPs) are the largest family of transcription factors in higher metazoans. They also represent the most diverse family with regards to the composition of their recognition sequences. Although there are a number of ZFPs with characterized DNA-binding preferences, the specificity of the vast majority of ZFPs is unknown and cannot be directly inferred by homology due to the diversity of recognition residues present within individual fingers. Given the large number of unique zinc fingers and assemblies present across eukaryotes, a comprehensive predictive recognition model that could accurately estimate the DNA-binding specificity of any ZFP based on its amino acid sequence would have great utility. Toward this goal, we have used the DNA-binding specificities of 678 two-finger modules from both natural and artificial sources to construct a random forest-based predictive model for ZFP recognition. We find that our recognition model outperforms previously described determinant-based recognition models for ZFPs, and can successfully estimate the specificity of naturally occurring ZFPs with previously defined specificities.
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