ArticleNucleic acids research2014
Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation.
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 42 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
42 citing papers in PubMed, 67 citations in OpenAlex.
- Human Synthetic Biology and Programmable Gene Regulation Control.Annual review of genomics and human genetics · 2025Review
- The generation of novel epialleles in plants: the prospective behind re-shaping the epigenome.Frontiers in plant science · 2025Review
- Reshaping the Landscape of the Genome: Toolkits for Precise DNA Methylation Manipulation and Beyond.JACS Au · 2024Review
- Development of Locus-Directed Editing of the Epigenome from Basic Mechanistic Engineering to First Clinical Applications.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Neuroepigenetic Editing.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Synthetic Epigenetic Reprogramming of Mesenchymal to Epithelial States Using the CRISPR/dCas9 Platform in Triple Negative Breast Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Review
- Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.Genome biology · 2022Article
- Epigenetic Editing in Prostate Cancer: Challenges and Opportunities.Epigenetics · 2022Review
- Broadly active zinc finger protein-guided transcriptional activation of HIV-1.Molecular therapy. Methods & clinical development · 2021Article
- Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing.Nucleic acids research · 2021Article
- Chromatin Manipulation and Editing: Challenges, New Technologies and Their Use in Plants.International journal of molecular sciences · 2021Review
- Epigenome engineering: new technologies for precision medicine.Nucleic acids research · 2020Article
- Regulation of IL12B Expression in Human Macrophages by TALEN-mediated Epigenome Editing.Current medical science · 2020Article
- Actinomycin D downregulates Sox2 and improves survival in preclinical models of recurrent glioblastoma.Neuro-oncology · 2020Article
- Transcriptional repression of PTEN in neural cells using CRISPR/dCas9 epigenetic editing.Scientific reports · 2020Article
- Site-Specific DNA Demethylation as a Potential Target for Cancer Epigenetic Therapy.Epigenetics insights · 2020Review
- Review
- Activating PTEN Tumor Suppressor Expression with the CRISPR/dCas9 System.Molecular therapy. Nucleic acids · 2019Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
Artificial transcription factors (ATFs) and genomic nucleases based on a DNA binding platform consisting of multiple zinc finger domains are currently being developed for clinical applications. However, no genome-wide investigations into their binding specificity have been performed. We have created six-finger ATFs to target two different 18 nt regions of the human SOX2 promoter; each ATF is constructed such that it contains or lacks a super KRAB domain (SKD) that interacts with a complex containing repressive histone methyltransferases. ChIP-seq analysis of the effector-free ATFs in MCF7 breast cancer cells identified thousands of binding sites, mostly in promoter regions; the addition of an SKD domain increased the number of binding sites ∼ 5-fold, with a majority of the new sites located outside of promoters. De novo motif analyses suggest that the lack of binding specificity is due to subsets of the finger domains being used for genomic interactions. Although the ATFs display widespread binding, few genes showed expression differences; genes repressed by the ATF-SKD have stronger binding sites and are more enriched for a 12 nt motif. Interestingly, epigenetic analyses indicate that the transcriptional repression caused by the ATF-SKD is not due to changes in active histone modifications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.