ArticleGenome biology and evolution2014
Deep vertebrate roots for mammalian zinc finger transcription factor subfamilies.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 80 citations in OpenAlex.
- 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
- A whole-genome scan for evidence of positive and balancing selection in aye-ayes (Daubentonia madagascariensis) utilizing a well-fit evolutionary baseline model.G3 (Bethesda, Md.) · 2025Article
- A whole-genome scan for evidence of recent positive and balancing selection in aye-ayes (bioRxiv : the preprint server for biology · 2024Article
- Comprehensive Annotation and Expression Profiling of C2H2 Zinc Finger Transcription Factors across Chicken Tissues.International journal of molecular sciences · 2024Article
- Gene expression networks regulated by human personality.Molecular psychiatry · 2024Review
- Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy.iScience · 2024Article
- A zinc finger transcription factor enables social behaviors while controlling transposable elements and immune response in prefrontal cortex.Translational psychiatry · 2024Article
- Primate-specific ZNF808 is essential for pancreatic development in humans.Nature genetics · 2023Article
- PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets.Molecular biology and evolution · 2023Article
- 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
- Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells.International journal of molecular sciences · 2023Article
- Editorial: Exploring impacts of combined exposures to particles and chemicals on immune reactions across living organisms.Frontiers in toxicology · 2023Article
- Article
- Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds.Scientific reports · 2022Article
- Active endogenous retroviral elements in human pluripotent stem cells play a role in regulating host gene expression.Nucleic acids research · 2022Article
- The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain.International journal of molecular sciences · 2022Article
- KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences.Mobile DNA · 2022Article
- Loss of zinc-finger protein 212 leads to Purkinje cell death and locomotive abnormalities with phospholipase D3 downregulation.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
While many vertebrate transcription factor (TF) families are conserved, the C2H2 zinc finger (ZNF) family stands out as a notable exception. In particular, novel ZNF gene types have arisen, duplicated, and diverged independently throughout evolution to yield many lineage-specific TF genes. This evolutionary dynamic not only raises many intriguing questions but also severely complicates identification of those ZNF genes that remain functionally conserved. To address this problem, we searched for vertebrate "DNA binding orthologs" by mining ZNF loci from eight sequenced genomes and then aligning the patterns of DNA-binding amino acids, or "fingerprints," extracted from the encoded ZNF motifs. Using this approach, we found hundreds of lineage-specific genes in each species and also hundreds of orthologous groups. Most groups of orthologs displayed some degree of fingerprint divergence between species, but 174 groups showed fingerprint patterns that have been very rigidly conserved. Focusing on the dynamic KRAB-ZNF subfamily--including nearly 400 human genes thought to possess potent KRAB-mediated epigenetic silencing activities--we found only three genes conserved between mammals and nonmammalian groups. These three genes, members of an ancient familial cluster, encode an unusual KRAB domain that functions as a transcriptional activator. Evolutionary analysis confirms the ancient provenance of this activating KRAB and reveals the independent expansion of KRAB-ZNFs in every vertebrate lineage. Most human ZNF genes, from the most deeply conserved to the primate-specific genes, are highly expressed in immune and reproductive tissues, indicating that they have been enlisted to regulate evolutionarily divergent biological traits.
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