ArticleGenome biology2023
Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 18 citations in OpenAlex.
- Brassinosteroids promote sugar synthesis by inhibiting BIN2 phosphorylation of phosphoenolpyruvate carboxykinase.Nature plants · 2026Article
- Genome-wide modelling of plant transcription factor binding captures regulatory variants associated with phenotypic traits.Nature communications · 2026Article
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.Nature genetics · 2025Article
- UPL3 promotes BZR1 degradation, growth arrest, and seedling survival under starvation stress in Arabidopsis.Plant communications · 2025Article
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions.G3 (Bethesda, Md.) · 2025Article
- Benchmark of chromatin-protein interaction methods in haploid round spermatids.Frontiers in cell and developmental biology · 2025Article
- Evolutionary trajectory of transcription factors and selection of targets for metabolic engineering.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Genome-Wide Association Studies Reveal That the Abietane Diterpene Isopimaric Acid Promotes Rice Growth through Inhibition of Defense Pathways.International journal of molecular sciences · 2024Article
- Natural variations of heterosis-related allele-specific expression genes in promoter regions lead to allele-specific expression in maize.BMC genomics · 2024Article
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Authors and funding
13 authors at 6 institutions in 2 countries.
Funding
Abstract
backgroundGenetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches.
resultsHere, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits.
conclusionOur study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.
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