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

First author: Wenhao Yan; Affiliations: Humboldt-Universität zu Berlin (柏林洪堡大学): Berlin, Germany

Corresponding author: Kerstin Kaufmann 

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.

增强子对于发育时期特异性基因的表达尤其重要，但其在植物基因组中的动态调控仍不清楚。本文中，作者比较了拟南芥在花发育过程中全基因组范围上的H3K27ac定位、染色质开放程度以及基因转录变化。H3K27ac能够标记近启动子区，说明拟南芥中H3K27ac并不是增强子的特征。作者通过数据分析和分子试验证明了I型DNA酶超敏性位点可作为增强子的标记。作者预测的增强子在花发育的不同阶段存在高度的特异性，并且显著与开花相关表型的SNPs相关，并且在不同十字花科植物中十分保守。通过全基因组转录因子结合位点数据，作者发现开花主要调控子和发育阶段特异性转录因子主要富集在发育动态波动的增强子区。最终，作者进一步鉴定了显著与由开花调控转录因子介导的发育阶段特异性基因调控相关的增强子类别及内含子增强子。本文的研究揭示了增强子在植物发育过程中的功能柔性，同时也提供了详尽的植物增强子注释。

通讯：Kerstin Kaufmann (https://www2.hu-berlin.de/biologie/flower/)

个人简介：2001-2005年，耶拿大学，博士。

研究方向：植物发育过程中的转录调控网络。

doi: https://doi.org/10.1038/s41467-019-09513-2

Journal: Nature Communications

First Published: April 12, 2019