ArticleNature communications2025
Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- Dynamic chromatin accessibility reveals BrKAN2 as a key regulator of Chinese cabbage leaf heading.Molecular horticulture · 2026Article
- Comparative Genomics Reveals Evolutionary Constraints of Regulatory Elements in theAnimals : an open access journal from MDPI · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution.iScience · 2026Review
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression.aBIOTECH · 2025Article
- Gene-LLMs: a comprehensive survey of transformer-based genomic language models for regulatory and clinical genomics.Frontiers in genetics · 2025Review
- Beyond the genome: the role of functional markers in contemporary plant breeding.Frontiers in plant science · 2025Review
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Comparative genomic studies can identify genes under evolutionary constraint or specialized for trait innovation. Growing evidence suggests that evolutionary constraint also acts on non-coding regulatory sequences, exerting significant impacts on fitness-related traits, although it has yet to be thoroughly explored in plants. Using the assay for transposase-accessible chromatin by sequencing (ATAC-seq), we profile over 80,000 maize accessible chromatin regions (ACRs), revealing that ACRs evolve faster than coding genes, with about one-third being maize-specific and regulating genes associated with speciation. We highlight the role of transposable elements (TEs) in driving intraspecific innovation of ACRs and identify hundreds of candidate ACRs potentially involved in transcriptional rewiring during maize domestication. Additionally, we demonstrate the importance of accessible chromatin in maintaining subgenome dominance and controlling complex trait variations. This study establishes a framework for analyzing the evolutionary trajectory of plant regulatory sequences and offers candidate loci for downstream exploration and application in maize breeding.
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Registered trials
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