ArticleNature communications2020
Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 114 papers.
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
114 citing papers in PubMed, 234 citations in OpenAlex.
- Predicting transcriptional regulators in plants in the era of artificial intelligence.Current opinion in plant biology · 2026Review
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- CasY7: An optimized Cas12i system for enhanced genome editing in monocot crops.Journal of integrative plant biology · 2026Article
- Genome-Wide and GWAS Dissection of Maize Fibrillin Genes Reveals Plastid Regulators of Drought and Salt Stress Tolerance.Current issues in molecular biology · 2026Article
- Designed Alleles of ZmRap2.7 Decouple the Trade-Off Between Early Flowering and Yield Penalty.Plant biotechnology journal · 2026Article
- Genome-wide modelling of plant transcription factor binding captures regulatory variants associated with phenotypic traits.Nature communications · 2026Article
- The incomplete dominance of gene expression controlled by Trans-eQTL hotspots contributes to heterosis in maize.Nature communications · 2026Article
- A novel genetic framework reveals transcriptional "butterfly effect" underlying heterosis in maize.Journal of advanced research · 2026Article
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- The landscape of regulatory element evolution in a C4 perennial grass.BMC genomics · 2026Article
- Deep learning-based semantic matching of cis-regulatory DNA sequences facilitates the prediction of gene function.Nature plants · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.bioRxiv : the preprint server for biology · 2025Article
- Decades' progress and prospects on maize functional genomics and molecular breeding.Science China. Life sciences · 2025Review
- 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
54 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
11 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The transcription regulatory network inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex network. In this study, we use large-scale ChIP-seq to reconstruct it in the maize leaf, and train machine-learning models to predict TF binding and co-localization. The resulting network covers 77% of the expressed genes, and shows a scale-free topology and functional modularity like a real-world network. TF binding sequence preferences are conserved within family, while co-binding could be key for their binding specificity. Cross-species comparison shows that core network nodes at the top of the transmission of information being more conserved than those at the bottom. This study reveals the complex and redundant nature of the plant transcription regulatory network, and sheds light on its architecture, organizing principle and evolutionary trajectory.
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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 Socratic graph.