ArticleNature protocols2014
A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue.
Article in Nature protocols, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- A MYB-Related Transcriptional Module Cooperatively Represses Xylem Development in Poplar.Plant biotechnology journal · 2026Article
- miR172-AP2 Controls Age-Dependent Regeneration Competence in Populus.Plant biotechnology journal · 2026Article
- ZmSSRP1-mediated chromatin accessibility modulates maize development via regulation of ZmBRD1 transcription.Plant physiology · 2026Article
- CsPRMT5-mediated histone H4R3 dimethylation negatively regulates resistance to gray blight in tea plants (Horticulture research · 2025Article
- Epigenetic regulation of lignin biosynthesis in wood formation.The New phytologist · 2025Article
- PcWRKY1 Represses Transcription of Yellow Stripe-Like 3 (PcYSL3) to Negatively Regulate Radial Cadmium Transport in Poplar Stems.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The transcriptional regulation of a putative hemicellulose gene, PtrPARVUS2 in poplar.Scientific reports · 2024Article
- Growth-regulating factor 15-mediated vascular cambium differentiation positively regulates wood formation in hybrid poplar (Frontiers in plant science · 2024Article
- Comprehensive Analysis of the Catalase (International journal of molecular sciences · 2023Article
- Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds.Tree physiology · 2023Article
- Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis.Plant biotechnology journal · 2022Article
- Role of PsnWRKY70 in Regulatory Network Response to Infection withInternational journal of molecular sciences · 2022Article
- Dimerization of PtrMYB074 and PtrWRKY19 mediates transcriptional activation of PtrbHLH186 for secondary xylem development in Populus trichocarpa.The New phytologist · 2022Article
- Protoplast isolation and transcriptome analysis of developing xylem in Pinus massoniana (Pinaceae).Molecular biology reports · 2022Article
- A PtrLBD39-mediated transcriptional network regulates tension wood formation inPlant communications · 2022Article
- A Cys2His2 Zinc Finger Transcription FactorFrontiers in plant science · 2022Article
- PagWOX11/12a activates PagCYP736A12 gene that facilitates salt tolerance in poplar.Plant biotechnology journal · 2021Article
- High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy.Horticulture research · 2021Article
- Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood.Plant physiology · 2021Article
- ThHSFA1 Confers Salt Stress Tolerance through Modulation of Reactive Oxygen Species Scavenging by Directly RegulatingInternational journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
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Abstract
Woody cells and tissues are recalcitrant to standard chromatin immunoprecipitation (ChIP) procedures. However, we recently successfully implemented ChIP in wood-forming tissue of the model woody plant Populus trichocarpa. Here we provide the detailed ChIP protocol optimized for wood-forming tissue that we used in those studies. By using stem-differentiating xylem (SDX; a wood-forming tissue), we identified all steps that were ineffective in standard ChIP protocols and systematically modified them to develop and optimize a robust ChIP protocol. The protocol includes tissue collection, cross-linking, nuclear isolation, chromatin extraction, DNA fragmentation, immunoprecipitation, DNA purification and sequence analysis. The protocol takes 2.5 d to complete and allows a robust 8-10-fold enrichment of transcription factor (TF)-bound genomic fragments (~150 ng/g of SDX) over nonspecific DNAs. The enriched DNAs are of high quality and can be used for subsequent PCR and DNA-seq analyses. We used this protocol to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation. Our protocol, which may be suitable for many tissue types, is so far the only working ChIP system for wood-forming tissue.
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