ArticleGenome research2015
CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Targeting SUV39H2 exon skipping reverses resistance to CDK4/6 inhibitors via transcriptional activation of p21.Science advances · 2026Article
- A bivalent molecular glue linking lysine acetyltransferases to oncogene-induced cell death.Cell · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- CRISPR Gene Tagging for Illuminating Endogenous Protein Dynamics.International journal of molecular sciences · 2026Review
- Review
- The Disordered Region of ASXL1 Acts as an Auto-Regulator Through Condensation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Decoding RNA-Protein Interactions: Methodological Advances and Emerging Challenges.Advanced genetics (Hoboken, N.J.) · 2025Review
- The sotos syndrome gene Nsd1 safeguards developmental gene enhancers poised for transcription by maintaining the precise deposition of histone methylation.The Journal of biological chemistry · 2025Article
- Unmeasured human transcription factor ChIP-seq data shape functional genomics and demand strategic prioritization.Briefings in functional genomics · 2025Article
- An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome.PloS one · 2025Article
- BPDCN MYB fusions regulate cell cycle genes, impair differentiation, and induce myeloid-dendritic cell leukemia.JCI insight · 2024Article
- Rapid and dynamic detection of endogenous proteins through in locus tagging in rice.Plant communications · 2024Article
- Targeting the chromatin binding of exportin-1 disrupts NFAT and T cell activation.Nature chemical biology · 2024Article
- C646 degrades Exportin-1 to modulate p300 chromatin occupancy and function.Cell chemical biology · 2024Article
- Probabilistic association of differentially expressed genes withGenome research · 2024Article
- Distinct regulatory networks control toxin gene expression in elapid and viperid snakes.BMC genomics · 2024Article
- An efficient and cost-effective method for disrupting genes in RAW264.7 macrophages using CRISPR-Cas9.PloS one · 2024Article
- CRISPR-Based Therapies: Revolutionizing Drug Development and Precision Medicine.Current gene therapy · 2024Review
- Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells.Genome research · 2023Article
- Genome-wide census of ATF4 binding sites and functional profiling of trait-associated genetic variants overlapping ATF4 binding motifs.PLoS genetics · 2023Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade antibodies, and the vast majority of commercially available antibodies fail to generate usable data sets. To ameliorate these technical obstacles, we present a robust methodological approach for performing ChIP-seq through epitope tagging of endogenous TFs. We used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based genome editing technology to develop CRISPR epitope tagging ChIP-seq (CETCh-seq) of DNA-binding proteins. We assessed the feasibility of CETCh-seq by tagging several DNA-binding proteins spanning a wide range of endogenous expression levels in the hepatocellular carcinoma cell line HepG2. Our data exhibit strong correlations between both replicate types as well as with standard ChIP-seq approaches that use TF antibodies. Notably, we also observed minimal changes to the cellular transcriptome and to the expression of the tagged TF. To examine the robustness of our technique, we further performed CETCh-seq in the breast adenocarcinoma cell line MCF7 as well as mouse embryonic stem cells and observed similarly high correlations. Collectively, these data highlight the applicability of CETCh-seq to accurately define the genome-wide binding profiles of DNA-binding proteins, allowing for a straightforward methodology to potentially assay the complete repertoire of TFs, including the large fraction for which ChIP-quality antibodies are not available.
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Registered trials
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