ArticleGenome biology2017
Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.Nature methods · 2026Article
- Characterization of C2H2 superfamily expansions in cephalopods and their contribution to nervous system evolution.iScience · 2025Article
- 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
- Production of Homogeneous, Functional Zinc-Finger Arrays in High Yield With Two Chromatographic Steps.Bio-protocol · 2025Article
- New Drosophila promoter-associated architectural protein Mzfp1 interacts with CP190 and is required for housekeeping gene expression and insulator activity.Nucleic acids research · 2024Article
- An integrative approach to protein sequence design through multiobjective optimization.PLoS computational biology · 2024Article
- An integrative approach to protein sequence design through multiobjective optimization.bioRxiv : the preprint server for biology · 2024Article
- Genetic features and genomic targets of human KRAB-zinc finger proteins.Genome research · 2023Article
- Transposable elements drive the evolution of metazoan zinc finger genes.Genome research · 2023Article
- RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific.Scientific reports · 2023Article
- Article
- Adaptive evolvability through direct selection instead of indirect, second-order selection.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2022Review
- Function and Evolution of C1-2i Subclass of C2H2-Type Zinc Finger Transcription Factors in POPLAR.Genes · 2022Article
- Article
- Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182.ACS omega · 2022Article
- Characterization and evolutionary origin of novel CHaematologica · 2021Article
- Article
- Bioinformatics of Metalloproteins and Metalloproteomes.Molecules (Basel, Switzerland) · 2020Review
- The geometric influence on the Cys2His2 zinc finger domain and functional plasticity.Nucleic acids research · 2020Article
- Similarity regression predicts evolution of transcription factor sequence specificity.Nature genetics · 2019Article
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7 authors.
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Abstract
backgroundThe C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown.
resultsHere, we show that the C2H2-ZF expansion in metazoans is facilitated by contribution of non-base-contacting residues to DNA binding energy, allowing base-contacting specificity residues to mutate without catastrophic loss of DNA binding. In contrast, C2H2-ZF DNA binding in fungi, plants, and other lineages is constrained by reliance on base-contacting residues for DNA-binding functionality. Reconstructions indicate that virtually every DNA triplet was recognized by at least one C2H2-ZF domain in the common progenitor of placental mammals, but that extant C2H2-ZF domains typically bind different sequences from these ancestral domains, with changes facilitated by non-base-contacting residues.
conclusionsOur results suggest that the evolution of C2H2-ZFs in metazoans was expedited by the interaction of non-base-contacting residues with the DNA backbone. We term this phenomenon "kaleidoscopic evolution," to reflect the diversity of both binding motifs and binding motif transitions and the facilitation of their diversification.
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