This Article Free via Open Access: OA Figures Only OA Full Text Full Text (PDF) Supporting Information Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a colleague Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Add to My File Cabinet Download to citation manager Request Copyright Permission Citing Articles Citing Articles via HighWire Citing Articles via CrossRef Citing Articles via Google Scholar Google Scholar Articles by Wright, M. A. Articles by Segrè, D. Search for Related Content PubMed PubMed Citation Articles by Wright, M. A. Articles by Segrè, D. Social Bookmarking                What's this?

 Previous Article  | Table of Contents |  Next Article 

BIOLOGICAL SCIENCES / GENETICS
Chromosomal periodicity of evolutionarily conserved gene pairs

Matthew A. Wright^*,, Peter Kharchenko, George M. Church^*, and Daniel Segrè^,¶

*Department of Genetics, Harvard–Massachusetts Institute of Technology Division of Health Sciences and Technology, and Harvard–Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA 02115; and Departments of Biology and Biomedical Engineering, and Bioinformatics Program, Boston University, Boston, MA 02215

Edited by John R. Roth, University of California, Davis, CA, and approved May 11, 2007 (received for review December 6, 2006)

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.

chromosome structure | computational genomics | nucleoid | spatial organization

Author contributions: M.A.W., G.M.C., and D.S. designed research; M.A.W., P.K., and D.S. performed research; P.K. contributed new reagents/analytic tools; M.A.W., P.K., G.M.C., and D.S. analyzed data; and M.A.W. and D.S. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/cgi/content/full/0610776104/DC1.

^¶To whom correspondence should be addressed. E-mail: dsegre{at}bu.edu

© 2007 by The National Academy of Sciences of the USA

CiteULike    Complore    Connotea    Del.icio.us    Digg    What's this?

This article has been cited by other articles in HighWire Press-hosted journals:

				G. Kolesov, Z. Wunderlich, O. N. Laikova, M. S. Gelfand, and L. A. Mirny How gene order is influenced by the biophysics of transcription regulation PNAS, August 28, 2007; 104(35): 13948 - 13953. [Abstract] [Full Text] [PDF]

Current Issue | Archives | Online Submission | Info for Authors | Editorial Board | About Subscribe | Advertise | Contact | Site Map Copyright © 2007 by the National Academy of Sciences