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

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. Overall design: 48 mRNA-seq libraries were sequenced

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