ArticleGenome biology2020
The regulatory landscape of early maize inflorescence development.
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 40 papers.
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Who cites it
40 citing papers in PubMed, 61 citations in OpenAlex.
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- SEdb 3.0: a comprehensive super-enhancer database across multiple species.Nucleic acids research · 2026Article
- From Structure to Function of Promoters and 5'UTRs in Maize.International journal of molecular sciences · 2026Review
- Novel genome editing approaches to manipulate apical meristem activity for crop yield.Frontiers in plant science · 2026Review
- Rational design of promoter editing confers multipathogen resistance in rice.Genome biology · 2025Article
- Graphene oxide enhances aphid resistance in sorghum via the miR319-SbTCP7-SbLOX3 Pathway.Plant biotechnology journal · 2025Article
- Transcription factor binding divergence drives transcriptional and phenotypic variation in maize.Nature plants · 2025Article
- ZmSSRP1 facilitates the progression of RNA polymerase II and is essential for kernel development in maize.The Plant cell · 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
- Full-length transcriptome provides insights into the molecular regulation of seed spike number inFrontiers in plant science · 2025Article
- Brassinosteroid biosynthesis and signaling: Conserved and diversified functions of core genes across multiple plant species.Plant communications · 2024Review
- Establishment and Maintenance of Heat-Stress Memory in Plants.International journal of molecular sciences · 2024Review
- Photosynthetic capacity and assimilate transport of the lower canopy influence maize yield under high planting density.Plant physiology · 2024Article
- Underground communication: Long non-coding RNA signaling in the plant rhizosphere.Plant communications · 2024Review
- Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation.bioRxiv : the preprint server for biology · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundThe functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments.
resultHere, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen- and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6% of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3' ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates.
conclusionsThese analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.
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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.