ArticleCommunications biology2020
Reverse Chromatin Immunoprecipitation (R-ChIP) enables investigation of the upstream regulators of plant genes.
Article in Communications biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 18 citations in OpenAlex.
- Direct and high-yield chromatin isolation by SBCP unlocks superior plant proteomics and epigenomic profiling.Plant cell reports · 2026Article
- A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest.Genome research · 2026Review
- An efficient screening system of disease-resistant genes from wild apple, Malus sieversii in response to Valsa mali pathogenic fungus.Plant methods · 2023Article
- Review
- NF-κB Transcriptional Activity Indispensably Mediates Hypoxia-Reoxygenation Stress-Induced microRNA-210 Expression.International journal of molecular sciences · 2023Article
- Phishing alert! A Cas9-based method reveals the identity of promoter-bound transcription factors.Plant physiology · 2023Article
- A reverse chromatin immunoprecipitation technique based on the CRISPR-dCas9 system.Plant physiology · 2023Article
- Single-Molecule Detection of Nucleic Acids via Liposome Signal Amplification in Mass Spectrometry.Sensors (Basel, Switzerland) · 2022Article
- Transcriptional Regulation of Ripening in Chili Pepper Fruits (International journal of molecular sciences · 2021Review
- Recent Advances in the Roles of HSFs and HSPs in Heat Stress Response in Woody Plants.Frontiers in plant science · 2021Review
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA binding proteins carry out important and diverse functions in the cell, including gene regulation, but identifying these proteins is technically challenging. In the present study, we developed a technique to capture DNA-associated proteins called reverse chromatin immunoprecipitation (R-ChIP). This technology uses a set of specific DNA probes labeled with biotin to isolate chromatin, and the DNA-associated proteins are then identified using mass spectrometry. Using R-ChIP, we identified 439 proteins that potentially bind to the promoter of the Arabidopsis thaliana gene AtCAT3 (AT1G20620). According to functional annotation, we randomly selected 5 transcription factors from these candidates, including bZIP1664, TEM1, bHLH106, BTF3, and HAT1, to verify whether they in fact bind to the AtCAT3 promoter. The binding of these 5 transcription factors was confirmed using chromatin immunoprecipitation quantitative real-time PCR and electrophoretic mobility shift assays. In addition, we improved the R-ChIP method using plants in which the DNA of interest had been transiently introduced, which does not require the T-DNA integration, and showed that this substantially improved the protein capture efficiency. These results together demonstrate that R-ChIP has a wide application to characterize chromatin composition and isolate upstream regulators of a specific gene.
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