Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-23686 - Genome-wide binding of replication initiation proteins in Bacillus subtilis

Status
Released on 7 December 2010, last updated on 2 May 2014
Organism
Bacillus subtilis
Samples (48)
Array (1)
Protocols (10)
Description
Initiation of DNA replication requires binding of the initiator protein, DnaA, to specific binding sites in the chromosomal origin of replication, oriC. In low G+C Gram-positive bacteria, the primosomal proteins DnaD and DnaB, in conjunction with loader ATPase DnaI, load the replicative helicase at oriC, and this depends on DnaA. DnaD and DnaB are also required to load the replicative helicase outside of oriC during replication restart, in a DnaA-independent manner. DnaA also binds to many sites around the chromosome, outside of oriC, and acts as a transcription factor at several of these. Using chromatin immunoprecipitation, we found that DnaD and DnaB, but not the replicative helicase, are associated with many of the chromosomal regions bound by DnaA in vivo in Bacillus subtilis. This association was dependent on DnaA and the order of recruitment was the same as that at oriC, but was independent of a functional oriC. The presence of DnaD and DnaB at the secondary (non-oriC) targets of DnaA in the absence of helicase loading indicates a possible role for DnaD and DnaB in modulating the activity of DnaA. The genome-wide binding profiles of DnaA, DnaD, DnaB and DnaC were determined. Binding profiles were determined in exponentially growing cells with and without HPUra treatment. Three biological replicates were analyzed per protein/treatment (one per array). Enrichment in immunoprecipitated samples versus total genomic DNA were determined.
Experiment type
ChIP-chip by array 
Contacts
Alan D. Grossman <clee2@mit.edu>, Alan D Grossman, Carla Y Bonilla, Houra Merrikh, Wiep K Smits
Citation
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-23686.idf.txt
Sample and data relationshipE-GEOD-23686.sdrf.txt
Raw data (1)E-GEOD-23686.raw.1.zip
Processed data (1)E-GEOD-23686.processed.1.zip
Array designA-GEOD-10707.adf.txt
Links