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Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis
Wenhao Yan1, Dijun Chen2,3, Julia Schumacher1,4
1Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
Nature Communications
|April 14, 2019
Summary
Plant enhancers control gene expression during development. This study identifies distal regulatory elements as key enhancers in Arabidopsis flower development, revealing their dynamic roles and association with flowering traits.
Area of Science:
- Plant biology
- Genomics
- Developmental biology
Background:
- Enhancers are crucial for stage-specific gene expression, but their regulation in plants is not well understood.
- Histone modifications like H3K27ac are often associated with enhancers in animals, but their role in plants requires clarification.
Purpose of the Study:
- To investigate the genome-wide localization of H3K27ac, chromatin accessibility, and transcriptomic changes during Arabidopsis flower development.
- To identify and characterize plant enhancers and their regulatory roles in flower development.
Main Methods:
- Genome-wide analysis of H3K27ac, chromatin accessibility (DNase I hypersensitive sites), and transcriptomics.
- Computational prediction and experimental validation of enhancers.
- Integration with transcription factor binding data.
Main Results:
- H3K27ac predominantly marks promoter-proximal regions, not distal enhancers in Arabidopsis.
- Distal DNase I hypersensitive sites accurately predict enhancers.
- Predicted enhancers show high stage-specificity during flower development and are conserved in related species.
- Floral master regulators and stage-specific transcription factors bind to dynamic enhancers, regulating stage-specific gene expression.
Conclusions:
- Distal regulatory elements, identified via chromatin accessibility, function as enhancers in Arabidopsis flower development.
- Enhancers are dynamically regulated by transcription factors during plant development.
- This study provides a framework for annotating plant enhancers and understanding their functional flexibility.
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