ArticleGenome biology2017
Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
112 citing papers in PubMed, 191 citations in OpenAlex.
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- KNOX II Transcription Factor HOS59 Regulates Gypsy Transposable Elements to Modulate Panicle Development in Rice.Plant, cell & environment · 2026Article
- Article
- Sgf29 regulates pluripotency by maintaining chromatin accessibility and promoting the expression of core transcription factors.Science China. Life sciences · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- The landscape of regulatory element evolution in a C4 perennial grass.BMC genomics · 2026Article
- From Natural Discovery to AI-Guided Design: A Curated Collection of Compact Enhancers for Crop Engineering.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- H3K4me1 directs H3K36me2 and H3K36me3 deposition in land plants.Nature communications · 2026Article
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- Coordinated epigenomic reprogramming and chromatin-mediated transcriptional regulation during soybean callus development.Frontiers in plant science · 2026Article
- A review of flavonoids at the crossroads of plant defense: integrating biotic and abiotic stress tolerance through AI- and CRISPR/Cas-guided metabolic reprogramming.Frontiers in plant science · 2026Review
- Nanorate sequencing reveals theProceedings of the National Academy of Sciences of the United States of America · 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
- Hybrids reveal accessible chromatinbioRxiv : the preprint server for biology · 2025Article
- A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution.Nature plants · 2025Article
- Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules.Journal of integrative plant biology · 2025Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Transcription factor binding divergence drives transcriptional and phenotypic variation in maize.Nature plants · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
52 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
11 authors at 7 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhile most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling. Here we show that integration of chromatin characteristics can be applied to predict distal enhancer candidates in Zea mays, thereby providing a basis for a better understanding of gene regulation in this important crop plant.
resultTo predict transcriptional enhancers in the crop plant maize (Zea mays L. ssp. mays), we integrated available genome-wide DNA methylation data with newly generated maps for chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac) enrichment in young seedling and husk tissue. Approximately 1500 intergenic regions, displaying low DNA methylation, high chromatin accessibility and H3K9ac enrichment, were classified as enhancer candidates. Based on their chromatin profiles, candidate sequences can be classified into four subcategories. Tissue-specificity of enhancer candidates is defined based on the tissues in which they are identified and putative target genes are assigned based on tissue-specific expression patterns of flanking genes.
conclusionsOur method identifies three previously identified distal enhancers in maize, validating the new set of enhancer candidates and enlarging the toolbox for the functional characterization of gene regulation in the highly repetitive maize genome.
Indexed as
Identifiers
What OpenQuestion holds
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.