ArticleNature communications2024
Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Machine learning for multi-omics data integration in crop improvement: a systematic review.BMC bioinformatics · 2026Pooled it
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- SERRATE Regulates Floral Meristem Activity by Antagonizing SHOOT MERISTEMLESS and Repressing Cytokinin Signaling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrated single cell transcriptomics analysis for unraveling heterogeneity and plasticity of root cells for sustainable and regenerative agriculture.Frontiers in plant science · 2026Review
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- A Natural Major Module Confers the Trade-Off between Phenotypic Mean and Plasticity of Grain Chalkiness in Rice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Review
- Modification of TAWAWA1-mediated panicle architecture by genome editing of a downstream conserved noncoding sequence in rice.Plant biotechnology journal · 2025Article
- Epitranscriptomic Control of Drought Tolerance in Rice: The Role of RNA Methylation.Plants (Basel, Switzerland) · 2025Review
- One versus many independent assemblies of symbiotic nitrogen fixation in flowering plants.Nature communications · 2025Review
- Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication.Nature communications · 2025Article
- The chromatin accessibility landscape during early maize seed development.The Plant journal : for cell and molecular biology · 2025Article
- Identification of QTLs for internode length and diameter associated with lodging resistance in rice.Frontiers in plant science · 2025Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for ~15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.
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