Fractal Topology of Gene Promoter Networks at Phase Transitions

Preston R. Aldrich, Robert K. Horsley, Yousuf A. Ahmed, Joseph J. Williamson and Stefan M. TurcicDepartment of Biological Sciences, Benedictine University, Lisle, IL 60532, USA. AbstractMuch is known regarding the structure and logic of genetic regulatory networks. Less understood is the contextual...

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Bibliographic Details
Published in:Gene regulation and systems biology 2010-07, Vol.2010 (4), p.75-82
Main Authors: Aldrich, Preston R., Horsley, Robert K., Ahmed, Yousuf A., Williamson, Joseph J., Turcic, Stefan M.
Format: Article
Language:English
Subjects:
Abundance
DNA
Escherichia coli
Fractals
Gene regulation
Genes
Genetic transcription
Language
Nodes
Nuclei
Original Research
Phase transition
Promoters
Promoters (Genetics)
Transcription initiation
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Summary:Preston R. Aldrich, Robert K. Horsley, Yousuf A. Ahmed, Joseph J. Williamson and Stefan M. TurcicDepartment of Biological Sciences, Benedictine University, Lisle, IL 60532, USA. AbstractMuch is known regarding the structure and logic of genetic regulatory networks. Less understood is the contextual organization of promoter signals used during transcription initiation, the most pivotal stage during gene expression. Here we show that promoter networks organize spontaneously at a dimension between the 1-dimension of the DNA and 3-dimension of the cell. Network methods were used to visualize the global structure of E. coli sigma (σ) recognition footprints using published promoter sequences (RegulonDB). Footprints were rendered as networks with weighted edges representing bp-sharing between promoters (nodes). Serial thresholding revealed phase transitions at positions predicted by percolation theory, and nuclei denoting short steps through promoter space with geometrically constrained linkages. The network nuclei are fractals, a power-law organization not yet described for promoters. Genome-wide promoter abundance also scaled as a power-law. We propose a general model for the development of a fractal nucleus in a transcriptional grammar.
ISSN:1177-6250
1177-6250
DOI:10.4137/GRSB.S5389