Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated genes in Arabidopsis

NAC transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) functions as a master regulator in DNA damage response of Arabidopsis. However, the signaling pathway controlled by SOG1 remains elusive. To identify genes whose expression is regulated by SOG1 in response to double strand breaks, wild-type (WT: Col-0 ecotype) and sog1-1 mutant plants were treated with or without zeocin for 2 h and were subjected to microarray analysis using Arabidopsis custom microarrays (GEO array platform: GPL19830). We found that 432 genes exhibited altered expressions in response to zeocin-induced double strand breaks in the SOG1-dependent manner. In addition, combining them with ChIP-Seq data, we identified 146 genes as SOG1-direct target genes. 2 week-old WT and sog1-1 mutant plants, grown in liquid MS medium under continuous light, were transferred to liquid MS medium with or without 15 µM zeocin and treated for 2 h. Two biological repeats of WT (mock), WT (zeocin-treated), sog1-1 (mock) and sog1-1 (zeocin-treated) whole plants were harvested and were subjected to microarray analysis.