title: Spatial features for Escherichia coli genome organization.
abstract: BACKGROUND
  In bacterial genomes, the compactly encoded genes and operons are well organized, with genes in the same biological pathway or operons in the same regulon close to each other on the genome sequence. In addition, the linearly close genes have a higher probability of co-expression and their protein products tend to form protein-protein interactions. However, the organization features of bacterial genomes in a three-dimensional space remain elusive. The DNA interaction data of Escherichia coli, measured by the genome conformation capture (GCC) technique, have recently become available, which allowed us to investigate the spatial features of bacterial genome organization.
  
  
  RESULTS
  By renormalizing the GCC data, we compared the interaction frequency of operon pairs in the same regulon with that of random operon pairs. The results showed that arrangements of operons in the E. coli genome tend to minimize the spatial distance between operons in the same regulon. A similar global organization feature exists for genes in biological pathways of E. coli. In addition, the genes close to each other spatially (even if they are far from each other on the genome sequence) tend to be co-expressed and form protein-protein interactions. These results provided new insights into the organization principles of bacterial genomes and support the notion of transcription factory.
  
  
  CONCLUSIONS
  This study revealed the organization features of Escherichia coli genomic functional units in the 3D space and furthered our understanding of the link between the three-dimensional structure of chromosomes and biological function.
authors: National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China. 774918771@qq.com.
authors: Ting
authors: T
authors: Xie
authors: National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China. liangyu.fu@foxmail.com.
authors: Liang-Yu
authors: LY
authors: Fu
authors: National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China. yqy@mail.hzau.edu.cn.
authors: Qing-Yong
authors: QY
authors: Yang
authors: National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China. 651153763@qq.com.
authors: Heng
authors: H
authors: Xiong
authors: National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China. 15071469218@163.com.
authors: Hongrui
authors: H
authors: Xu
authors: National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China. mbg@mail.hzau.edu.cn.
authors: Bin-Guang
authors: BG
authors: Ma
authors: National Key Laboratory of Crop Genetic Improvement, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China. zhy630@mail.hzau.edu.cn.
authors: Hong-Yu
authors: HY
authors: Zhang
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D009876:Operon / Q000235:genetics; D060066:Protein Interaction Maps / Q000235:genetics*
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