Spatial features for Escherichia coli genome organization

详细信息    查看全文

• 作者：Ting Xie ; Liang-Yu Fu ; Qing-Yong Yang ; Heng Xiong ; Hongrui Xu ; Bin-Guang Ma…
• 关键词：Escherichia coli ; Chromosome architecture ; Genome organization ; Co ; expression ; Protein–protein interactions
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：2,247 KB
• 参考文献：1. Jacob F, Perrin D, Sánchez C, Monod J. Operon: a group of genes with the expression coordinated by an operator. CR Hebd Seances Acad Sci. 1960;250:1727-.
  2. Lercher MJ, Hurst LD. Co-expressed yeast genes cluster over a long range but are not regularly spaced. J Mol Biol. 2006;359(3):825-1. CrossRef
  3. Dossena S, Nofziger C, Bernardinelli E, Soyal S, Patsch W, Paulmichl M. Use of the operon structure of the C. elegans genome as a tool to identify functionally related proteins. Cell Physiol Biochem. 2013;32(7):41-6. CrossRef
  4. Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 2001;11(3):356-2. CrossRef
  5. Yin Y, Zhang H, Olman V, Xu Y. Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome. Proc Natl Acad Sci USA. 2010;107(14):6310-. CrossRef
  6. Zhang H, Yin Y, Olman V, Xu Y. Genomic arrangement of regulons in bacterial genomes. PLoS One. 2012;7(1):e29496. CrossRef
  7. Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013;14(6):390-03. CrossRef
  8. Hakim O, Sung M-H, Voss TC, Splinter E, John S, Sabo PJ, et al. Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements. Genome Res. 2011;21(5):697-06. CrossRef
  9. Krivega I, Dean A. Enhancer and promoter interactions—long distance calls. Curr Opin Genet Dev. 2012;22(2):79-5. CrossRef
  10. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376-0. CrossRef
  11. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, et al. Three-Dimensional folding and functional organization principles of the / drosophila genome. Cell. 2012;148(3):458-2. CrossRef
  12. Le TB, Imakaev MV, Mirny LA, Laub MT. High-resolution mapping of the spatial organization of a bacterial chromosome. Science. 2013;342(6159):731-. CrossRef
  13. Cagliero C, Grand RS, Jones MB, Jin DJ, O’Sullivan JM. Genome conformation capture reveals that the / Escherichia coli chromosome is organized by replication and transcription. Nucleic Acids Res. 2013;41(12):6058-1. CrossRef
  14. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-. CrossRef
  15. Bardet AF, He Q, Zeitlinger J, Stark A. A computational pipeline for comparative ChIP-seq analyses. Nat Protoc. 2011;7(1):45-1. CrossRef
  16. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):1-. CrossRef
  17. Rogozin IB, Makarova KS, Murvai J, Czabarka E, Wolf YI, Tatusov RL, et al. Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res. 2002;30(10):2212-3. CrossRef
  18. Williams EJ, Bowles DJ. Coexpression of neighboring genes in
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

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.