The SOG1 transcriptional activator and the MYB3R family of repressors control a complex gene network in response to DNA damage in Arabidopsis [RNA-seq myb3r135 vs wt]

To combat DNA damage, organisms mount a DNA Damage Response (DDR) that results in cell cycle regulation, DNA repair, and, in severe cases, cell death. Underscoring the importance of gene regulation in this response, studies in Arabidopsis have demonstrated that all the aforementioned processes rely on SUPRESSOR OF GAMMA 1 (SOG1), a NAC transcription factor (TF). However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data corresponds to single time-point snapshots. Here, we generated transcriptional models of the DDR from gamma-irradiated ([gamma]-IR) wild-type and sog1 seedlings during a 24-hour timecourse using DREM, the Dynamic Regulatory Events Miner. In the wild-type model, the NAC and MYB3R TF families are implicated in the induction and repression of damage responsive genes, respectively, and the 2,400 differentially expressed genes form 11 subgroups with distinct expression profiles, biological functions, and cis-regulatory features. Within this network, SOG1 acts as a transcriptional activator, directly targeting 300 genes, including TFs, DNA repair factors, and cell cycle regulators, and, indirectly influencing the expression of most, but not all, of the remaining [gamma]-IR-responsive genes. Among these indirect targets are many cell cycle genes that are repressed by the MYB3R TFs after DNA damage and group together within the DREM model, linking these TFs to specific expression subgroups. Together, this transcriptional roadmap of the DDR provides insight into many [gamma]-IR-responsive genes and reveals the first layer of interactions connecting SOG1 to the diverse processes coordinated in response to DNA damage.

为应对DNA损伤，生物会启动DNA损伤应答（DNA Damage Response, DDR），该应答可介导细胞周期调控、DNA修复，在损伤严重时还会触发细胞死亡。基因调控在该应答过程中的重要性已得到多项研究证实：拟南芥相关研究表明，上述所有过程均依赖于γ射线应答抑制因子1（SUPRESSOR OF GAMMA 1, SOG1）——一种NAC类转录因子（Transcription Factor, TF）。然而，将SOG1与上述下游过程关联的表达调控网络在很大程度上仍未被阐明；尽管DNA损伤应答的发生时长覆盖数分钟至数小时，但现有多数转录组数据仅为单个时间点的静态快照。本研究利用动态调控事件挖掘器（Dynamic Regulatory Events Miner, DREM），对经γ射线辐照（γ-IR）的野生型与sog1突变体幼苗开展24小时时间序列采样，构建了DNA损伤应答的转录调控模型。在野生型模型中，NAC与MYB3R转录因子家族分别参与损伤响应基因的激活与抑制；本次鉴定得到的2400个差异表达基因可划分为11个亚组，各亚组具备独特的表达谱、生物学功能及顺式调控特征。在该调控网络中，SOG1作为转录激活因子，直接靶向包括转录因子、DNA修复因子及细胞周期调控因子在内的300个基因，并间接影响绝大多数（而非全部）剩余的γ-IR响应基因的表达。其中，大量细胞周期相关基因属于这类间接靶向基因：这类基因在DNA损伤后会被MYB3R转录因子抑制，并在DREM模型中聚为一类，从而将MYB3R转录因子与特定的表达亚组建立了关联。综上，本研究构建的DNA损伤应答转录调控图谱，为解析众多γ-IR响应基因提供了全新视角，并首次揭示了SOG1与DNA损伤应答相关的各类协调过程之间的相互作用层级。