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Series GSE112529 Query DataSets for GSE112529
Status Public on Nov 15, 2018
Title 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]
Organism Arabidopsis thaliana
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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 6 ChIP-seq libraries were sequenced
 
Contributor(s) Bourbousse C, Law J
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Submission date Mar 30, 2018
Last update date Jan 23, 2019
Contact name Julie Ann Law
E-mail(s) jlaw@salk.edu
Phone 8584534100
Organization name The Salk Institute for Biological Studies
Department PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY
Lab Law Lab
Street address 10010 North Torrey Pines Rd
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (6)
GSM3072264 input_SOG1-3xFLAG_20min
GSM3072265 input_SOG1-3xFLAG_1h
GSM3072266 IP_SOG1-3xFLAG_20min
This SubSeries is part of SuperSeries:
GSE112773 The SOG1 transcriptional activator and the MYB3R repressors control a complex gene network in response to DNA damage in Arabidopsis
Relations
BioProject PRJNA448141
SRA SRP136806

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE112529_RAW.tar 230.1 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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