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]
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PROVIDER: PRJNA448146 | ENA |
REPOSITORIES: ENA
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Project description: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.
2018-11-15 | GSE112529 | GEO
Project description: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.
2018-11-15 | GSE112531 | GEO
Project description: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.
2018-11-15 | GSE112748 | GEO
Project description: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.
2018-11-15 | GSE112544 | GEO
Project description: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.
2018-11-15 | GSE112543 | GEO
Project description:The SOG1 transcriptional activator and the MyB3R family of repressors control a complex gene network in response to DNA damage in Arabidopsis [SOG1 ChIP-seq]
| PRJNA448141 | ENA
Project description: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 of the aforementioned processes rely on SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a NAC family transcription factor (TF) that has been functionally equated to the mammalian tumor suppressor, p53. However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data correspond to single time-point snapshots. Here, we generated transcriptional models of the DDR from GAMMA (?)-irradiated wild-type and sog1 seedlings during a 24-hour time course using DREM, the Dynamic Regulatory Events Miner, revealing 11 coexpressed gene groups with distinct biological functions and cis-regulatory features. Within these networks, additional chromatin immunoprecipitation and transcriptomic experiments revealed that SOG1 is the major activator, directly targeting the most strongly up-regulated genes, including TFs, repair factors, and early cell cycle regulators, while three MYB3R TFs are the major repressors, specifically targeting the most strongly down-regulated genes, which mainly correspond to G2/M cell cycle-regulated genes. Together these models reveal the temporal dynamics of the transcriptional events triggered by ?-irradiation and connects these events to TFs and biological processes over a time scale commensurate with key processes coordinated in response to DNA damage, greatly expanding our understanding of the DDR.
| S-EPMC6310815 | biostudies-literature
Project description:The SOG1 transcriptional activator and the MYB3R repressors control a complex gene network in response to DNA damage in Arabidopsis
| PRJNA448926 | ENA
Project description:The SOG1 transcriptional activator and the MYB3R family of repressors control a complex gene network in response to DNA damage in Arabidopsis [RNA-seq t vs t0]
| PRJNA448925 | ENA
Project description: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]
| PRJNA448158 | ENA