Gene-centered regulatory networks

Abstract

Differential gene expression plays a critical role in the development and physiology of multicellular organisms. At a 'systems level' (e.g. at the level of a tissue, organ or whole organism), this process can be studied using gene regulatory network (GRN) models that capture physical and regulatory interactions between genes and their regulators. In the past years, significant progress has been made toward the mapping of GRNs using a variety of experimental and computational approaches. Here, we will discuss gene-centered approaches that we employed to characterize GRNs and describe insights that we have obtained into the global design principles of gene regulation in complex metazoan systems.

Figure 1:

Cartoon illustrating hypothetical interactions in a GRN, which combines physical and regulatory interactions between TFs and their target genes. In addition to TFs, other regulators need to be incorporated such as microRNAs and transcriptional cofactors.

Figure 2:

GRNs can be delineated using two conceptually different, but highly complementary approaches. TF-centered methods start with a TF of interest and identify DNA fragments this TF binds to. Gene-centered methods start with a set of DNA fragments and identify the TFs these fragments interact with.

Figure 3:

Gateway-compatible Y1H assays provide a convenient gene-centered method for GRN mapping. A yeast DNA bait strain contains two reporter constructs integrated into its genome. Each construct contains the same DNA fragment, but different reporter genes, such as HIS3 and LacZ. A cDNA or TF library can be used as a prey resource, or collections of TFs can be tested individually. The panel on the right shows the readout of a Y1H experiment. AD alone indicates the negative control used to assess DNA bait background growth on media lacking histidine and containing 3-AT, and background bait coloring on a βGal assay. Different interacting TFs confer different interaction phenotypes; i.e. light blue versus dark blue.

Figure 4:

GRNs can be analyzed at the whole network level, for instance by determining individual and global connectivities. (A) A compiled GRN of ∼200 C. elegans gene promoters (based on our published data). This model reflects the complexity of systems level gene regulation. Circles—TFs, diamonds, diamonds—target gene promoters, edges—protein–DNA interactions as determined by Y1H assays. This visualization was done using Cytoscape v.2.6 software with ‘random layout’ settings, which randomly distributes the nodes in a given network. (B) Top—analysis of incoming or outgoing degrees of individual nodes reveals network hubs. Middle—TOC analysis and clustering can reveal TF modules. Bottom—examples of network motifs that are overrepresented in GRNs. Circles—TFs, diamonds—target gene promoters, hairpin structure—miRNA gene promoters.