ArticleThe Plant cell2012
Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis.
Article in The Plant cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
132 citing papers in PubMed, 1 synthesis or guideline pooled it, 227 citations in OpenAlex.
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- Article
- Cross-species optimization of nuclei isolation in ten plant species.Plant methods · 2026Article
- Big data approaches to understanding gene regulatory networks in the shoot apical meristem andFrontiers in plant science · 2026Review
- Synthetic promoter design in plants: integration of computational and experimental approaches.Frontiers in plant science · 2026Review
- Single-molecule views of chromatin accessibility and structure during photomorphogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Organ-level gene-regulatory networks inferred from transcriptomic data reveal context-specific regulation and highlight novel regulators of ripening and ABA-mediated responses in tomato.Plant communications · 2025Article
- Transcription Factors in Plant Gene Expression Regulation.International journal of molecular sciences · 2025Article
- Abscisic acid and GIGANTEA signalling converge to regulate the recruitment of CONSTANS to the FT promoter and activate floral transition.Journal of experimental botany · 2025Article
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Functional Characterization of Accessible Chromatin in Common Wheat.International journal of molecular sciences · 2024Article
- Molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato.The Plant cell · 2024Article
- Genome organization and botanical diversity.The Plant cell · 2024Review
- An epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis.PLoS genetics · 2024Article
- Petal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases.Nature communications · 2024Article
- Estimating genome-wide DNA methylation heterogeneity with methylation patterns.Epigenetics & chromatin · 2023Article
- Dynamics ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- 3D organization of regulatory elements for transcriptional regulation in Arabidopsis.Genome biology · 2023Article
- Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton.BMC biology · 2023Article
72 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
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression and regulation in eukaryotes is controlled by orchestrated binding of regulatory proteins, including both activators and repressors, to promoters and other cis-regulatory DNA elements. An increasing number of plant genomes have been sequenced; however, a similar effort to the ENCODE project, which aimed to identify all functional elements in the human genome, has yet to be initiated in plants. Here we report genome-wide high-resolution mapping of DNase I hypersensitive (DH) sites in the model plant Arabidopsis thaliana. We identified 38,290 and 41,193 DH sites in leaf and flower tissues, respectively. The DH sites were depleted of bulk nucleosomes and were tightly associated with RNA polymerase II binding sites. Approximately 90% of the binding sites of two well-characterized MADS domain transcription factors, APETALA1 and SEPALLATA3, were covered by the DH sites. We demonstrate that protein binding footprints within a specific genomic region can be revealed using the DH site data sets in combination with known or putative protein binding motifs and gene expression data sets. Thus, genome-wide DH site mapping will be an important tool for systematic identification of all cis-regulatory DNA elements in plants.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.