Spatial patterns of transcriptional activity in the chromosome of Escherichia coli -: art. no. R86

被引:133
作者
Jeong, KS [1 ]
Ahn, J [1 ]
Khodursky, AB [1 ]
机构
[1] Univ Minnesota, Dept Biochem Mol Biol & Biophys, St Paul, MN 55108 USA
关键词
D O I
10.1186/gb-2004-5-11-r86
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Although genes on the chromosome are organized in a fixed order, the spatial correlations in transcription have not been systematically evaluated. We used a combination of genomic and signal processing techniques to investigate the properties of transcription in the genome of Escherichia coli K12 as a function of the position of genes on the chromosome. Results: Spectral analysis of transcriptional series revealed the existence of statistically significant patterns in the spatial series of transcriptional activity. These patterns could be classified into three categories: short-range, of up to 16 kilobases (kb); medium-range, over 100-125 kb; and long-range, over 600-800 kb. We show that the significant similarities in gene activities extend beyond the length of an operon and that local patterns of coexpression are dependent on DNA supercoiling. Unlike short-range patterns, the formation of medium and long-range transcriptional patterns does not strictly depend on the level of DNA supercoiling. The long-range patterns appear to correlate with the patterns of distribution of DNA gyrase on the bacterial chromosome. Conclusions: Localization of structural components in the transcriptional signal revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome. The demonstration that spatial patterns of transcription could be modulated pharmacologically and genetically, along with the identification of molecular correlates of transcriptional patterns, offer for the first time strong evidence of physiologically determined higher-order organization of transcription in the bacterial chromosome.
引用
收藏
页数:10
相关论文
共 47 条
  • [1] Genome-scale analysis of the uses of the Escherichia coli genome:: Model-driven analysis of heterogeneous data sets
    Allen, TE
    Herrgård, MJ
    Liu, MZ
    Qiu, Y
    Glasner, JD
    Blattner, FR
    Palsson, BO
    [J]. JOURNAL OF BACTERIOLOGY, 2003, 185 (21) : 6392 - 6399
  • [2] [Anonymous], GENE EXPRESSION OMNI
  • [3] Spurious spatial periodicity of co-expression in microarray data due to printing design
    Balázsi, G
    Kay, KA
    Barabási, AL
    Oltvai, ZN
    [J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (15) : 4425 - 4433
  • [4] The complete genome sequence of Escherichia coli K-12
    Blattner, FR
    Plunkett, G
    Bloch, CA
    Perna, NT
    Burland, V
    Riley, M
    ColladoVides, J
    Glasner, JD
    Rode, CK
    Mayhew, GF
    Gregor, J
    Davis, NW
    Kirkpatrick, HA
    Goeden, MA
    Rose, DJ
    Mau, B
    Shao, Y
    [J]. SCIENCE, 1997, 277 (5331) : 1453 - +
  • [5] Box G.E. P., 1994, Time Series Analysis: Forecasting Control, V3rd
  • [6] Exploring the new world of the genome with DNA microarrays
    Brown, PO
    Botstein, D
    [J]. NATURE GENETICS, 1999, 21 (Suppl 1) : 33 - 37
  • [7] A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression
    Cohen, BA
    Mitra, RD
    Hughes, JD
    Church, GM
    [J]. NATURE GENETICS, 2000, 26 (02) : 183 - 186
  • [8] TRANSCRIPTION REGULATES OXOLINIC ACID-INDUCED DNA GYRASE CLEAVAGE AT SPECIFIC SITES ON THE ESCHERICHIA-COLI CHROMOSOME
    CONDEMINE, G
    SMITH, CL
    [J]. NUCLEIC ACIDS RESEARCH, 1990, 18 (24) : 7389 - 7396
  • [9] Courcelle J, 2001, GENETICS, V158, P41
  • [10] Efron B., 1998, INTRO BOOTSTRAP