title: Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription.
abstract: 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.
authors: Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
authors: Cedric
authors: C
authors: Cagliero
authors: Ralph S
authors: RS
authors: Grand
authors: M Beatrix
authors: MB
authors: Jones
authors: Ding J
authors: DJ
authors: Jin
authors: Justin M
authors: JM
authors: O'Sullivan
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism; D001665:Binding Sites; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism; D002876:Chromosomes, Bacterial / Q000737:chemistry* / Q000378:metabolism; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000378:metabolism; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D018741:Replication Origin; D012694:Serine / Q000031:analogs & derivatives / Q000494:pharmacology; D014158:Transcription, Genetic
chemical_list: D001425:Bacterial Outer Membrane Proteins; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C533037:MatP protein, E coli; C089746:SeqA protein, E coli; C028002:serine hydroxamate; D012694:Serine
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