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

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

2005-04-18

arxiv.org/abs/q-bio/0504025v2

Trends Genet, 21:492-495, 2005

Biology

Quantitative Biology

Molecular Networks

Trends Genet (in press), main text 1, supplementary notes 1, 40 pages, 7 tables, 4 figs, minor modifications

Scientific paper

10.1016/j.tig.2005.06.013

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.

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