ArticlePlant methods2020
A native chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in strawberry fruits.
Article in Plant methods, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 24 citations in OpenAlex.
- FaRIF as a key regulator of strawberry fruit ripening: deciphering its targets and interaction networks.Horticulture research · 2026Article
- Chromatin Immunoprecipitation in Crops.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The H3K27me3 histone mark correlates with repression of colour and aroma development post-harvest in strawberry fruit.Journal of experimental botany · 2025Article
- Advances in Cellular and Molecular Biology Assays: A Review of Gold Standard Methods.International journal of innovative science and research technology · 2025Article
- Dynamic histone modification signatures coordinate developmental programs in strawberry fruit ripening.Horticulture research · 2024Article
- A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization.Molecular systems biology · 2024Article
- Inhibition of histone deacetylase in Arabidopsis root calli promotesFrontiers in plant science · 2024Article
- H3K4me3 changes occur in cell wall genes during the development ofFrontiers in plant science · 2024Article
- SET Domain Group 703 Regulates Planthopper Resistance by Suppressing the Expression of Defense-Related Genes.International journal of molecular sciences · 2023Article
- An efficient chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in peach reproductive tissues.Plant methods · 2022Article
- Characterization of expansin genes and their transcriptional regulation by histone modifications in strawberry.Planta · 2021Review
- OsIRO3 Plays an Essential Role in Iron Deficiency Responses and Regulates Iron Homeostasis in Rice.Plants (Basel, Switzerland) · 2020Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundCovalent modifications of histones and histone variants have great influence on chromatin structure, which is involved in the transcriptional regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful tool for studying in vivo DNA-histone interactions. Strawberry is a model for Rosaceae and non-climacteric fruits, in which histone modifications have been implicated to affect fruit development and ripening. However, a validated ChIP method has not been reported in strawberry, probably due to its high levels of polysaccharides which affect the quality of prepared chromatin and the efficiency of immunoprecipitation.
resultsWe describe a native chromatin immunoprecipitation (N-ChIP) protocol suitable for strawberry by optimizing the parameters for nuclei isolation, chromatin extraction, DNA fragmentation and validation analysis using quantitative real-time PCR (qRT-PCR). The qRT-PCR results show that both the active mark H3K36me3 and the silent mark H3K9me2 are efficiently immunoprecipitated for the enriched regions. Compared to X-ChIP (cross-linked chromatin followed by immunoprecipitation), our optimized N-ChIP procedure has a higher signal-to-noise ratio and a lower background for both the active and the silent histone modifications. Furthermore, high-throughput sequencing following N-ChIP demonstrates that nearly 90% of the enriched H3K9/K14ac peaks are overlapped between biological replicates, indicating its remarkable consistency and reproducibility.
conclusionsAn N-ChIP method suitable for the fleshy fruit tissues of woodland strawberry
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