Biology Reference
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biomolecules is a daunting task. Here, I will focus specifically on C. elegans gene
regulatory networks that control gene expression at the transcriptional and post-
transcriptional levels. I will briefly discuss the methods that can be used to identify
the players in gene regulatory networks, as well as approaches to identify interac-
tions between them, with a primary focus on gene-centered yeast one-hybrid (Y1H)
assays that are used to identify interactions between non-coding regulatory DNA
regions and TFs.
II. Gene Regulatory Networks
Gene regulatory networks are composed of two main components: nodes and
edges. The network nodes are the players involved, that is, the genes and their
regulators. The edges are the physical and/or regulatory relationships between the
nodes ( Fig. 2 B). Gene regulatory networks are different from better-known protein-
protein interaction networks, because gene regulatory networks are both bipartite
and directional. They are bipartite because there are two types of nodes: genes and
regulators, although of course some genes are themselves regulators of other genes
or proteins. Gene regulatory networks are directional because regulators control
genes and usually not the other way around. In order to map and characterize gene
regulatory networks, one needs to first identify the nodes. For the genes this means to
identify the non-coding genomic DNA sequences that participate in the control of
gene expression, and for the regulators this means to identify which protein-coding
genes encode TFs, RNA binding proteins, and other regulators, as well as to deter-
mine the complete collection of regulatory RNA molecules. Here, I will mostly
focus on TFs and microRNAs, and the types of genic regions they interact with.
III. Identifying Gene Regulatory Network Nodes
A. Regulatory Regions
Different parts of a gene can contribute to its regulation. The more complex an
organism, the more complex its gene regulation is. In C. elegans there are two main
regulatory regions: gene promoters in the genome and 3 0 UTRs in mRNAs.
1. Promoters
A gene promoter is the genomic DNA sequence immediately upstream of the
transcription start site. Generally, promoters are composed of a basal element where
the general transcriptional machinery binds (e.g., RNA polymerase II and general
TFs), and the proximal gene promoter that serves as a landing site for regulatory TFs.
Since the majority of C. elegans genes are subject to trans-splicing, precise tran-
scription start sites have not been determined for most genes. However, 5 0 UTRs are
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