General organisational principles of the transcriptional regulation system: a tree or a circle?

Recent advances of systemic approaches to gene expression and cellular metabolism provide unforeseen opportunities for relating and integrating extensive datasets describing the transcriptional regulation system as a whole. However, due to the multifaceted nature of the phenomenon, these datasets of...

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Bibliographic Details
Published in:Molecular bioSystems 2010-01, Vol.6 (4), p.662-676
Main Authors: Muskhelishvili, Georgi, Sobetzko, Patrick, Geertz, Marcel, Berger, Michael
Format: Article
Language:English
Subjects:
DNA, Bacterial - genetics
DNA, Bacterial - metabolism
DNA-Directed RNA Polymerases - genetics
DNA-Directed RNA Polymerases - metabolism
Escherichia coli - genetics
Escherichia coli - metabolism
Escherichia coli Proteins - genetics
Escherichia coli Proteins - metabolism
Gene Regulatory Networks
Genome, Bacterial
Homeostasis
Metabolic Networks and Pathways
Models, Biological
Models, Genetic
Systems Biology
Transcription, Genetic
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Summary:Recent advances of systemic approaches to gene expression and cellular metabolism provide unforeseen opportunities for relating and integrating extensive datasets describing the transcriptional regulation system as a whole. However, due to the multifaceted nature of the phenomenon, these datasets often contain logically distinct types of information determined by underlying approach and adopted methodology of data analysis. Consequently, to integrate the datasets comprising information on the states of chromatin structure, transcriptional regulatory network and cellular metabolism, a novel methodology enabling interconversion of logically distinct types of information is required. Here we provide a holistic conceptual framework for analysis of global transcriptional regulation as a system coordinated by structural coupling between the transcription machinery and DNA topology, acting as interdependent sensors and determinants of metabolic functions. In this operationally closed system any transition in physiological state represents an emergent property determined by shifts in structural coupling, whereas genetic regulation acts as a genuine device converting one logical type of information into the other.
ISSN:1742-206X
1742-2051
DOI:10.1039/b909192k