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

Wenhao Yan (1) , Dijun Chen (1, 2) , Julia Schumacher (1, 2) , Diego Durantini (2) , Julia Engelhorn (3) , Ming Chen (4) , Cristel Carles (3) , Kerstin Kaufmann (1)

1 Institut of Biology, Department of Plant Cellular and Molecular Biology
2 Institute of Biochemistry and Biology University of Potsdam
3 ChromDev - Dynamiques Chromatiniennes et Transitions Développementales
4 Department of Bioinformatics, College of Life Sciences, Zhejiang University

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.

Mots clés: Plant; Arabidopsis thaliana; Rice; Flower development; Gene expression

Domaines: Biochimie, Biologie Moléculaire

Wenhao Yan, Dijun Chen, Julia Schumacher, Diego Durantini, Julia Engelhorn, et al.. Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis. Nature Communications, 2019, 10 (1), pp.1705. ⟨10.1038/s41467-019-09513-2⟩. ⟨hal-02130228⟩