title: Chromosomal periodicity of evolutionarily conserved gene pairs.
abstract: Chromosomes are compacted hundreds of times to fit in the cell, packaged into dynamic folds whose structures are largely unknown. Here, we examine patterns in gene locations to infer large-scale features of bacterial chromosomes. Specifically, we analyzed >100 genomes and identified thousands of gene pairs that display two types of evolutionary correlations: a tendency to co-occur and a tendency to be located close together in many genomes. We then analyzed the detailed distribution of these pairs in Escherichia coli and found that genes in a pair tend to be separated by integral multiples of 117 kb along the genome and to be positioned in a 117-kb grid of genomic locations. In addition, the most pair-dense locations coincide with regions of intense transcriptional activity and the positions of top transcribed and conserved genes. These patterns suggest that the E. coli chromosome may be organized into a 117-kb helix-like topology that localizes a subset of the most essential and highly transcribed genes along a specific face of this structure. Our approach indicates an evolutionarily maintained preference in the spacing of genes along the chromosome and offers a general comparative genomics framework for studying chromosome structure, broadly applicable to other organisms.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Matthew A
authors.initials: MA
authors.lastname: Wright
authors.forename: Peter
authors.initials: P
authors.lastname: Kharchenko
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.forename: Daniel
authors.initials: D
authors.lastname: Segrè
mesh_terms: D002875:Chromosomes / Q000235:genetics*; D002876:Chromosomes, Bacterial; D015825:Chromosomes, Fungal; D017124:Conserved Sequence / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D005583:Fourier Analysis; D023061:Gene Order; D005798:Genes, Bacterial; D005800:Genes, Fungal; D017238:Genes, Helminth; D023281:Genomics; D008957:Models, Genetic; D010802:Phylogeny; D014158:Transcription, Genetic