ArticlePlant physiology2013
Measuring Arabidopsis chromatin accessibility using DNase I-polymerase chain reaction and DNase I-chip assays.
Article in Plant physiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- The chromatin accessibility landscape during early maize seed development.The Plant journal : for cell and molecular biology · 2025Article
- Linker histone H1 modulates defense priming and immunity in plants.Nucleic acids research · 2023Article
- Histone Deacetylase TaHDT701 Functions in TaHDA6-TaHOS15 Complex to Regulate Wheat Defense Responses toInternational journal of molecular sciences · 2020Article
- The Evening Complex Establishes Repressive Chromatin Domains Via H2A.Z Deposition.Plant physiology · 2020Article
- A tribute to Lars Hennig (1970-2018).Journal of experimental botany · 2018Article
- Parallel Evolution of Common Allelic Variants Confers Flowering Diversity inThe Plant cell · 2018Article
- Arabidopsis RNA Polymerase V Mediates Enhanced Compaction and Silencing of Geminivirus and Transposon Chromatin during Host Recovery from Infection.Journal of virology · 2018Article
- Relaxed chromatin induced by histone deacetylase inhibitors improves the oligonucleotide-directed gene editing in plant cells.Journal of plant research · 2018Article
- A natural tandem array alleviates epigenetic repression of IPA1 and leads to superior yielding rice.Nature communications · 2017Article
- The histone deacetylase inhibitor Entinostat enhances polymer-mediated transgene expression in cancer cell lines.Biotechnology and bioengineering · 2016Article
- Effect of in ovo folic acid injection on hepatic IGF2 expression and embryo growth of broilers.Journal of animal science and biotechnology · 2016Article
- The WD40 Domain Protein MSI1 Functions in a Histone Deacetylase Complex to Fine-Tune Abscisic Acid Signaling.The Plant cell · 2016Article
- Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures.The Plant cell · 2015Article
- Transcription of nuclear organellar DNA in a model plant system.Genome biology and evolution · 2014Article
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Authors and funding
3 authors.
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Abstract
DNA accessibility is an important layer of regulation of DNA-dependent processes. Methods that measure DNA accessibility at local and genome-wide scales have facilitated a rapid increase in the knowledge of chromatin architecture in animal and yeast systems. In contrast, much less is known about chromatin organization in plants. We developed a robust DNase I-polymerase chain reaction (PCR) protocol for the model plant Arabidopsis (Arabidopsis thaliana). DNA accessibility is probed by digesting nuclei with a gradient of DNase I followed by locus-specific PCR. The reduction in PCR product formation along the gradient of increasing DNase I concentrations is used to determine the accessibility of the chromatin DNA. We explain a strategy to calculate the decay constant of such signal reduction as a function of increasing DNase I concentration. This allows describing DNA accessibility using a single variable: the decay constant. We also used the protocol together with AGRONOMICS1 DNA tiling microarrays to establish genome-wide DNase I sensitivity landscapes.
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