Self-organization of gene regulatory network motifs enriched with short transcript's half-life transcription factors

Network motifs, the recurring regulatory structural patterns in networks, are able to self-organize to produce networks. Three major motifs, feedforward loop, single input modules and bi-fan are found in gene regulatory networks. The large ratio of genes to transcription factors (TFs) in genomes leads to a sharing of TFs by motifs and is sufficient to result in network self-organization. We find a common design principle of these motifs: short transcript's half-life (THL) TFs are significantly enriched in motifs and hubs. This enrichment becomes one of the driving forces for the emergence of the network scale-free topology and allows the network to quickly adapt to environmental changes. Most feedforward loops and bi-fans contain at least one short THL TF, which can be seen as a criterion for self-assembling these motifs. We have classified the motifs according to their short THL TF content. We show that the percentage of the different motif subtypes varies in different cellular conditions.