Gene-Centered Regulatory Network Mapping - Caenorhabditis Elegans: Molecular Genetics and Development - page 267

CHAPTER 10
Gene-Centered Regulatory
Network Mapping
Albertha J.M. Walhout
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts
Medical School, USA
Abstract
I. Introduction
II. Gene Regulatory Networks
III. Identifying Gene Regulatory Network Nodes
A. Regulatory Regions
B. Regulators
C. Delineating Gene Regulatory Network Edges
IV. Gene Regulatory Network Visualization and Analysis
A. Gene Regulatory Network Validation
V. Future Challenges
Acknowledgments
References
Abstract
The Caenorhabditis elegans hermaphrodite is a complex multicellular animal
that is composed of 959 somatic cells. The C. elegans genome contains 20,000
protein-coding genes, 940 of which encode regulatory transcription factors (TFs). In
addition, the worm genome encodes more than 100 microRNAs and many other
regulatory RNA and protein molecules. Most C. elegans genes are subject to regu-
latory control, most likely by multiple regulators, and combined, this dictates the
activation or repression of the gene and corresponding protein in the relevant cells and
under the appropriate conditions. A major goal in C. elegans research is to determine
the spatiotemporal expression pattern of each gene throughout development and in
response to different signals, and to determine how this expression pattern is accom-
plished. Gene regulatory networks describe physical and/or functional interactions
between genes and their regulators that result in specific spatiotemporal gene expres-
sion. Such regulators can act at transcriptional or post-transcriptional levels. Here, I