Gene-Centered Regulatory Network Mapping - Caenorhabditis Elegans: Molecular Genetics and Development - page 268

will discuss the methods that can be used to delineate gene regulatory networks in
C. elegans. I will mostly focus on gene-centered yeast one-hybrid (Y1H) assays that
are used to map interactions between non-coding genic regions, such as promoters,
and regulatory TFs. The approaches discussed here are not only relevant to C. elegans
biology, but can also be applied to other model organisms and humans.
I. Introduction
Complex multicellular model organisms such as C. elegans need to faithfully
develop from a fertilized oocyte into a complete and fully functioning animal that is
composed of different cell and tissue types. After development is completed, meta-
zoan organisms also need mechanisms for homeostasis and to adequately respond to
physiological and environmental cues, in order to find mating partners, to detect
food, and to avoid pathogens. For correct functionality, cells and tissues need to
compute an appropriate biological output based on the input they receive. Such an
output can, for instance, be to differentiate, to move, or to enter the dauer stage.
Biological outputs result from interactions between the different biomolecules cells
and tissues contain, including the genome, proteins and RNA molecules as well as
small molecules such as metabolites.
Developmental and post-developmental processes are controlled, at least in part,
by the specific spatiotemporal expression of each of the 20,000 protein-coding
genes in the C. elegans genome. Each gene/protein is likely controlled by multiple
regulators and at multiple levels ( Figs. 1 and 2 ). First, genes are transcribed into
Fig. 1 The different levels of differential gene expression. This review focuses mainly on the transcrip-
tion, and to a lesser extent, on microRNAs.