The noncoding RNA HIDDEN TREASURE 1 promotes phytochrome B-dependent seed germination by repressing abscisic acid biosynthesis

背景回顾：Light is a major environmental factor for seed germination. Red-light-activated phytochrome B (phyB) promotes seed germination by modulating the dynamic balance of two phytohormones, gibberellic acid (GA) and abscisic acid (ABA). 

提出问题：How phyB modulates ABA biosynthesis after perceiving a light signal is not yet well understood. 

主要发现：Here, we identified the noncoding RNA HIDDEN TREASURE 1 (HID1) as a repressor of ABA biosynthesis acting downstream of phyBduring Arabidopsis thaliana seed germination. 

结果1-HID1的功能：Loss of HID1 function led to delayed phyB-dependent seed germination. 

结果2-HID1与phyB的关系：Photo-activated phyBpromoted the accumulation of HID1 in the radicle within 48 hours of imbibition. Our transcriptomics analysis showed that HID1 and phyB co-regulate the transcription of a common set of genes involved in ABA and GA metabolism. 

结果3-HID1的抑制子：Through a forward genetic screen, we identified three ABA biosynthesis genes, ABA DEFICIENT 1 (ABA1), ABA2, and ABA3, as suppressors of HID1. 

结果4-HID1-ATXR7-NCED9：We further demonstrated that HID1 directly inhibits the transcription of 9-CIS-EPOXYCAROTENOID DIOXYGENASE (NCED9), a gene encoding a key rate-limiting enzyme of ABA biosynthesis. HID1 interacts with ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), an H3K4me3 methyltransferase, inhibiting its occupancy and H3K4me3 modification at the NCED9 locus. 

结论：Our study reveals a nuclear mechanism of phyB signaling transmitted through HID1 to control the internal homeostasis of ABA and GA, which gradually optimizes the transcriptional network during seed germination.

光是影响种子萌发的主要环境因素。受红光激活的光敏色素phyB，通过调控赤霉素（GA）和脱落酸（ABA）之间的动态平衡，促进种子萌发。但是，phyB在感知光信号之后如何调控ABA的生物合成还不清楚。本文中，作者鉴定到了一个在拟南芥种子萌发过程中，作用于phyB下游的ABA生物合成抑制子，即非编码的RNA HID1。HID1功能缺失突变会导致依赖于phyB的种子萌发延迟。光激活的phyB能够在种子吸胀的48小时内促进HID1在胚根中的表达。转录组分析显示，HID1和phyB共调控一些参与ABA和GA代谢基因的转录。通过一个正向遗传学筛选试验，作者鉴定到了3个ABA生物合成基因ABA1、ABA2和ABA3是HID1的抑制子。作者进一步发现，HID1能够直接抑制ABA生物合成途径限速酶编码基因NCED9的转录。HID1与一个H3K4me3甲基转移酶ATXR7互作，抑制后者在NCED9位点上的占据，从而抑制其对NCED9的H3K4me3修饰。本文的研究结果揭示了一个核中的phyB信号转导机制，通过HID1控制内源GA和ABA的内稳态，从而在种子萌发过程中逐步优化转录网络。