Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis

Wenhao Yan, Dijun Chen (), Julia Schumacher, Diego Durantini, Julia Engelhorn, Ming Chen, Cristel C. Carles and Kerstin Kaufmann ()
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Wenhao Yan: Humboldt-Universität zu Berlin
Dijun Chen: Humboldt-Universität zu Berlin
Julia Schumacher: Humboldt-Universität zu Berlin
Diego Durantini: University of Potsdam
Julia Engelhorn: Université Grenoble Alpes (UGA), CNRS, CEA, INRA, IRIG-LPCV, 38000 Grenoble, France
Ming Chen: Zhejiang University
Cristel C. Carles: Université Grenoble Alpes (UGA), CNRS, CEA, INRA, IRIG-LPCV, 38000 Grenoble, France
Kerstin Kaufmann: Humboldt-Universität zu Berlin

Nature Communications, 2019, vol. 10, issue 1, 1-16

Abstract: Abstract Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase І hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers.

Date: 2019
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DOI: 10.1038/s41467-019-09513-2

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