State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
BMC Biol. 2022 Jul 21;20(1):165. doi: 10.1186/s12915-022-01362-8.
Enhancers are cis-regulatory elements present in eukaryote genomes, which constitute indispensable determinants of gene regulation by governing the spatiotemporal and quantitative expression dynamics of target genes, and are involved in multiple life processes, for instance during development and disease states. The importance of enhancer activity has additionally been highlighted for immune responses in animals and plants; however, the dynamics of enhancer activities and molecular functions in plant innate immunity are largely unknown. Here, we investigated the involvement of distal enhancers in early innate immunity in Arabidopsis thaliana.
A group of putative distal enhancers producing low-abundance transcripts either unidirectionally or bidirectionally are identified. We show that enhancer transcripts are dynamically modulated in plant immunity triggered by microbe-associated molecular patterns and are strongly correlated with open chromatin, low levels of methylated DNA, and increases in RNA polymerase II targeting and acetylated histone marks. Dynamic enhancer transcription is correlated with target early immune gene expression patterns. Cis motifs that are bound by immune-related transcription factors, such as WRKYs and SARD1, are highly enriched within upregulated enhancers. Moreover, a subset of core pattern-induced enhancers are upregulated by multiple patterns from diverse pathogens. The expression dynamics of putative immunity-related enhancers and the importance of WRKY binding motifs for enhancer function were also validated.
Our study demonstrates the general occurrence of enhancer transcription in plants and provides novel information on the distal regulatory landscape during early plant innate immunity, providing new insights into immune gene regulation and ultimately improving the mechanistic understanding of the plant immune system.
增强子是真核生物基因组中的顺式调控元件，是基因调控不可或缺的决定因素，通过调控靶基因的时空和定量表达动态，参与到多个生命过程中，例如在发育和疾病状态下。增强子活性在动植物的免疫反应中也具有重要意义；然而，植物先天免疫中增强子活性和分子功能的动态仍然知之甚少。在这里，我们研究了拟南芥早期先天免疫中远端增强子的作用。
鉴定出一组产生低丰度单向或双向转录本的假定远端增强子。我们表明，在微生物相关分子模式触发的植物免疫中，增强子转录物是动态调节的，并且与开放染色质、低甲基化 DNA 水平、RNA 聚合酶 II 靶向和乙酰化组蛋白标记的增加强烈相关。动态增强子转录与靶早期免疫基因表达模式相关。与免疫相关转录因子（如 WRKY 和 SARD1）结合的顺式基序在上调的增强子中高度富集。此外，一组核心模式诱导的增强子被来自不同病原体的多种模式上调。免疫相关增强子的表达动态以及 WRKY 结合基序对增强子功能的重要性也得到了验证。
我们的研究证明了增强子转录在植物中的普遍发生，并提供了关于早期植物先天免疫中远端调控景观的新信息，为免疫基因调控提供了新的见解，并最终提高了对植物免疫系统的机制理解。
