Book contents
- Frontmatter
- Dedication
- Contents
- Preface
- List of abbreviations
- 1 Introduction
- I Network Reconstruction
- 2 Network Reconstruction: The Concept
- 3 Network Reconstruction: The Process
- 4 Metabolism in Escherichia coli
- 5 Prokaryotes
- 6 Eukaryotes
- 7 Biochemical Reaction Networks
- 8 Metastructures of Genomes
- II Mathematical Properties of Reconstructed Networks
- III Determining the Phenotypic Potential of Reconstructed Networks
- IV Basic and Applied Uses
- V Conceptual Foundations
- 29 Epilogue
- References
- Index
8 - Metastructures of Genomes
from I - Network Reconstruction
Published online by Cambridge University Press: 05 February 2015
- Frontmatter
- Dedication
- Contents
- Preface
- List of abbreviations
- 1 Introduction
- I Network Reconstruction
- 2 Network Reconstruction: The Concept
- 3 Network Reconstruction: The Process
- 4 Metabolism in Escherichia coli
- 5 Prokaryotes
- 6 Eukaryotes
- 7 Biochemical Reaction Networks
- 8 Metastructures of Genomes
- II Mathematical Properties of Reconstructed Networks
- III Determining the Phenotypic Potential of Reconstructed Networks
- IV Basic and Applied Uses
- V Conceptual Foundations
- 29 Epilogue
- References
- Index
Summary
The universe may be a 4-dimensional soap bubble in an 11-dimensional space. Who knows?
– Christian Klixbull JørgensenWith the publication of the first full genome sequence in the mid 1990s, it became possible, in principle, to identify all the gene products involved in complex biological processes in a single organism. In practice, almost 17 years later, this has proven difficult to accomplish using just sequence information. A toolbox of molecular biology methods that are implemented on a genome-scale are now available and it allows us to measure many properties of a genome with unprecedented resolution. A workflow that systematically integrates these data types can lead to the definition of the transcription unit (TU) architecture of a genome. This information, in turn, enables the reconstruction of transcriptional regulatory networks (TRNs) and other features. The full application and integrative analysis of genome-wide measurements led to the concept of a metastructure of a prokaryotic genome as there are many more attributes to a genome than its sequence and 3D arrangement.
The Concept of a Metastructure
With the plethora of genome-scale measurement methods, genomes can be characterized at multiple different organizational levels. Genomes used to be thought of in terms of their base sequence and three-dimensional structure. It is now clear that there are many more dimensions to genome organization, use, and information content (Figure 8.1). This realization has led to the concept of a metastructure of a bacterial genome [74].
Detailed examination of genome-wide data sets results in the definition of structural, operational, and functional annotations [74, 349]. Structural genome annotation provides the foundation for further operational and functional annotation and consists of coding (open reading frames, or ORFs) and non-coding genes, as well as intergenic regions. Elucidating the precise structural genome annotation subsequently allows the decoding of the operational genome annotation, which consists of operons and TUs. As a higher level of genome organization, the operon structure is a key to deciphering the flow of information encoded in the genome. A functional genome annotation assigns a function to an ORF and describes the biochemical properties of the gene products.
- Type
- Chapter
- Information
- Systems BiologyConstraint-based Reconstruction and Analysis, pp. 134 - 148Publisher: Cambridge University PressPrint publication year: 2015