ArticleGenome biology2020
3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed, 114 citations in OpenAlex.
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- Novel genome editing approaches to manipulate apical meristem activity for crop yield.Frontiers in plant science · 2026Review
- Chromatin state architecture governs transcription factor accessibility across plant genomes.PLoS genetics · 2026Article
- Single-molecule views of chromatin accessibility and structure during photomorphogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Decades' progress and prospects on maize functional genomics and molecular breeding.Science China. Life sciences · 2025Review
- Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules.Journal of integrative plant biology · 2025Article
- A heat stress-responsive epigenome defines the dynamic 3D chromatin structure in Chinese cabbage.Plant physiology · 2025Article
- BMI1s interact with condensin complexes to regulate chromatin 3D structure and gene expression inaBIOTECH · 2025Article
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for 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
- Application and Progress of Genomics in Deciphering the Genetic Regulation Mechanisms of Plant Secondary Metabolites.Plants (Basel, Switzerland) · 2025Review
- Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication.Nature communications · 2025Article
- Regulatory variation controlling architectural pleiotropy in maize.Nature communications · 2025Article
- The chromatin accessibility landscape during early maize seed development.The Plant journal : for cell and molecular biology · 2025Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMaize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of differentially expressed genes determining ear and tassel architecture within the 3D genome context is largely unknown.
resultsWe identify 56,055 and 52,633 open chromatin regions (OCRs) in developing maize ear and tassel primordia using ATAC-seq and characterize combinatorial epigenome features around these OCRs using ChIP-seq, Bisulfite-seq, and RNA-seq datasets. Our integrative analysis of coordinated epigenetic modification and transcription factor binding to OCRs highlights the cis and trans regulation of differentially expressed genes in ear and tassel controlling inflorescence architecture. We further systematically map chromatin interactions at high-resolution in corresponding tissues using in situ digestion-ligation-only Hi-C (DLO Hi-C). The extensive chromatin loops connecting OCRs and genes provide a 3D view on cis- and trans-regulatory modules responsible for ear- and tassel-specific gene expression. We find that intergenic SNPs tend to locate in distal OCRs, and our chromatin interaction maps provide a potential mechanism for trait-associated intergenic SNPs that may contribute to phenotypic variation by influencing target gene expression through chromatin loops.
conclusionsOur comprehensive epigenome annotations and 3D genome maps serve as valuable resource and provide a deep understanding of the complex regulatory mechanisms of genes underlying developmental and morphological diversities between maize ear and tassel.
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