ArticleThe Plant cell2015
Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures.
Article in The Plant cell, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 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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Who cites it
101 citing papers in PubMed, 1 synthesis or guideline pooled it.
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- Coordinating structure-guided design and cis-regulatory optimization to engineer elite herbicide-tolerance alleles in crops.Nature plants · 2026Article
- p-LoopF is associated with chromatin looping in large introns of Ginkgo biloba.Cell research · 2026Article
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- Precision Editing of Cis-Regulatory Elements Drives Crops Quantitative Traits Genetic Improvement: From Functional Dissection to Intelligent Design.Rice (New York, N.Y.) · 2026Review
- Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean.The Plant cell · 2026Article
- From Natural Discovery to AI-Guided Design: A Curated Collection of Compact Enhancers for Crop Engineering.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Big data approaches to understanding gene regulatory networks in the shoot apical meristem andFrontiers in plant science · 2026Review
- A voyage of reprogrammable metabolic bioengineering reshapes plant defense: from editing tools to synthetic systems.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
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- Conservation and variability of long-range interactions in structurally diverse maize genomes.Nature communications · 2025Article
- Vegetative to generative1 (Vgt1) is an enhancer affecting flowering time and jasmonate signaling in maize by promoting the expression of Zea mays Related to APETALA 2.7.Plant physiology · 2025Article
- Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules.Journal of integrative plant biology · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- The SAS chromatin-remodeling complex mediates inflorescence-specific chromatin accessibility for transcription factor binding.Nucleic acids research · 2025Article
- Genetic basis of camouflage in an alpine plant and its long-term co-evolution with an insect herbivore.Nature ecology & evolution · 2025Article
41 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
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enhancers are important regulators of gene expression in eukaryotes. Enhancers function independently of their distance and orientation to the promoters of target genes. Thus, enhancers have been difficult to identify. Only a few enhancers, especially distant intergenic enhancers, have been identified in plants. We developed an enhancer prediction system based exclusively on the DNase I hypersensitive sites (DHSs) in the Arabidopsis thaliana genome. A set of 10,044 DHSs located in intergenic regions, which are away from any gene promoters, were predicted to be putative enhancers. We examined the functions of 14 predicted enhancers using the β-glucuronidase gene reporter. Ten of the 14 (71%) candidates were validated by the reporter assay. We also designed 10 constructs using intergenic sequences that are not associated with DHSs, and none of these constructs showed enhancer activities in reporter assays. In addition, the tissue specificity of the putative enhancers can be precisely predicted based on DNase I hypersensitivity data sets developed from different plant tissues. These results suggest that the open chromatin signature-based enhancer prediction system developed in Arabidopsis may serve as a universal system for enhancer identification 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.