E-GEOD-40304 - Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription

Status
Released on 1 May 2013, last updated on 2 June 2014
Organism
Escherichia coli str. K-12 substr. MG1655
Samples (4)
Array (1)
Protocols (7)
Description
To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci. A 4 chips study of exponentially growing wild type E. coli strain MG1655 grown in LB rich media or after induction of the stringent response by serine hydroxamate for 30 min. Two technical replicates, Three biological replicates mixed prior hybridization on the chip.
Experiment type
transcription profiling by array 
Contacts
cedric cagliero <geo@ncbi.nlm.nih.gov>, Beatrix M Jones, Cedric Cagliero, Ding J Jin, Justin M O'Sullivan, Ralph S Grand
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-40304.idf.txt
Sample and data relationshipE-GEOD-40304.sdrf.txt
Raw data (1)E-GEOD-40304.raw.1.zip
Processed data (1)E-GEOD-40304.processed.1.zip
Array designA-GEOD-10046.adf.txt
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