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

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

PROVIDER: PRJNA415786 | ENA |

REPOSITORIES: ENA

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

Project description: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.

2017-11-01 | GSE106154 | GEO

Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated and 1 (SOG1)-target genes in Arabidopsis

Project description:Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated and 1 (SOG1)-target genes in Arabidopsis

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Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1)-target genes in Arabidopsis

Project description:Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1)-target genes in Arabidopsis

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Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1)-target genes in Arabidopsis

Project description: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 target genes of SOG1, we used wild-type plants harboring the transgene ProSOG1:SOG1-Myc, which expresses the SOG1-Myc fusion gene under the 2-kb SOG1 promoter. It was previously demonstrated that SOG1-Myc can complement the sog1-1 mutation (Yoshiyama et al., 2013). After treatment of plants with 15 µM zeocin for 2 hours, chromatin fragments bound to SOG1-Myc were immunoprecipitated with the anti-Myc antibody, and were subjected to next generation sequencing. We identified 778 SOG1-binding peak summits, which displayed peak values 16-fold higher than those in wild-type plants without the transgene. The genomic regions between 5-kb upstream and downstream of each peak summit included 1514 genes among which we found SMR5, SMR7 and CYCB1;1 that were previously identified as SOG1 target genes (Yi et al., 2014; Weimer et al., 2016). Among 1514 genes identified by ChIP-sequencing, 146 genes were overlapped with the SOG1-regulated genes extracted from the microarray data (GSE106154); therefore, we concluded that the 146 genes are SOG1 ditrect target genes.

2017-11-02 | GSE106415 | GEO

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