GSE175875
Characterization of the Radiation Desiccation Response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses.
In this study, we mapped the DdrO regulon in Deinococcus radiodurans by using two genome-scale approaches, ChIP-seq and RNA-seq analyses. These approaches were performed to find additional DdrO targets sites that were not predicted by previous in silico analyses. To our knowledge, we present here the first ChIP-seq analysis performed at the genome level in D. radiodurans. Alignments of DNA sequences extracted from ChIP-seq analysis were also performed to compare the consensus motif found to the predicted DdrO-binding motif.  Our results show that the RDR regulon in D. radiodurans is more complex than previously thought and is composed of at least 35 genes, including such DNA and RNA metabolism proteins as RecG and HelD helicases, and the prokaryotic replicative DNA ligase LigA, but also new genes associated with different metabolic pathways, involved in translation or encoding proteins of unknown function. Overall design: For RNA-seq: 12 RNAseq samples with 3 replicates each separated between two experiments.Two time course experiments using ?ddrO strains complemented by ddrO expressed, under its own promoter, from a plasmid with wild type or thermosensitive replication.  For ChIP-seq: 3 ChIP-seq samples with 3 replicates for IP samples, one replicate for Input sample and  one replicate for Mock sample.