ArticleNature protocols2010
Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP).
Article in Nature protocols, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 215 papers, 1 of them a synthesis that pooled it.
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Who cites it
215 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Interplay among ZF-HD and GRF transcription factors during Arabidopsis leaf development.Plant physiology · 2023Pooled it
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- ARABIDOPSIS Bsister and SEEDSTICK MADS-box transcription factors modulate maternal nutrient flow for seed development in Arabidopsis.Nature communications · 2026Article
- The OsWRKY15-OsSUT3 Regulatory Module Enhances Rice Pollen Fertility by Mediating Sucrose Allocation to Anthers.Plant biotechnology journal · 2026Article
- Designed Alleles of ZmRap2.7 Decouple the Trade-Off Between Early Flowering and Yield Penalty.Plant biotechnology journal · 2026Article
- KNOX II Transcription Factor HOS59 Regulates Gypsy Transposable Elements to Modulate Panicle Development in Rice.Plant, cell & environment · 2026Article
- The Transcription Factor FgSge1 Harnesses the SAGA Complex to Activate Mycotoxin Biosynthesis and Fungal Virulence.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- PsAvh109 suppresses SA-triggered immunity by mimicking TPL function to disrupt mediator complex assembly.Nature communications · 2026Article
- Natural Negative Feedback Loops Confer Indica-Japonica Differentiation for Grain Size Homeostasis in Rice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- CUT&Tag for High-Resolution Epigenomic Profiling From a Low Amount ofPlant direct · 2026Article
- Occupancy-based mechanism is the chief mode of ROS1 function in preventing DNA hypermethylation.Nature plants · 2026Article
- A genetic module boosts grain yield and nitrogen use efficiency by improving nitrate transport in maize.Nature genetics · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Allelic Variation in Maize Malate Dehydrogenase 7 Shapes Promoter Methylation and Banded Leaf and Sheath Blight Resistance.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Yeast One-Hybrid (Y1H) Assay for Single Promoter-Transcription Factor Interaction in Higher Plants.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Protocols for Chromatin Immunoprecipitation Sequencing and qPCR to Investigate Pytohormone-Responsive Transcriptional Regulation in Plants.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Chromatin Immunoprecipitation in Crops.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Investigating cis-regulatory elements and gene expression in multiple tomato varieties using interpretable deep learning.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- SPOROCYTELESS/NOZZLE cooperates with MADS-domain transcription factors to regulate an auxin-dependent network controlling Megaspore-Mother-Cell differentiation.Nature communications · 2025Article
- AP1 is a pioneer transcription factor that programmes cell fate through MADS-domain protein tetramerisation.Genome biology · 2025Article
155 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences can be identified by direct sequencing (ChIP-SEQ) or hybridization to microarrays (ChIP-CHIP). Given the small amounts of DNA that are usually obtained in ChIP experiments, successful and reproducible sample processing is challenging. Here we provide a detailed procedure for ChIP of plant TFs, as well as protocols for sample preparation for ChIP-SEQ and for ChIP-CHIP. Our ChIP procedure is optimized for high signal-to-noise ratio starting with tissue fixation, followed by nuclei isolation, immunoprecipitation, DNA amplification and purification. We also provide a guide for primary data analysis of ChIP-SEQ data. The complete protocol for ChIP-SEQ/ChIP-CHIP sample preparation starting from plant harvest takes approximately 7 d.
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