Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks.
Bottom Line: The gene regulatory network (GRN) is the central decision-making module of the cell.BQS explains many of the small- and large-scale properties of GRNs, provides conditions for evolvable robustness, and highlights general features of transcriptional response.BQS is severely compromised in a human cancer cell line, suggesting that loss of BQS might underlie the phenotypic plasticity of cancer cells, and highlighting a possible sequence of GRN alterations concomitant with cancer initiation.
Affiliation: College of Life Sciences, University of Dundee, Dundee, United Kingdom firstname.lastname@example.org.Show MeSH
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Mentions: The ‘0 hr’ GRN was obtained under conditions comparable with the organisms discussed previously. Figure 8 shows that all the predictions of BQS are met at this time. As indicated by Figure 8A, the GRN has a very limited number of long feedback loops (only three with three or more genes), in striking contrast with the hundreds observed in randomly generated networks of the same link density. Interestingly, all of the long feedback loops depend on the transcriptional interaction between SFPI1 and E2F1 (Figure 8—figure supplement 1A–C). Notably E2F1 plays a crucial role in the cell cycle and is only transiently activated at commitment to cell division at the end of G1. Therefore, all of the long feedback loops detected are likely to be transient. Similarly, the number of incomplete feedback loops is very small, and much lower than would be expected in random networks (Figure 8B). Motif analysis is also consistent with BQS: there is a much higher proportion of unregulated transcription factors than would be expected by chance (Figure 8E), and the proportion of stable 3- and 4-node motifs is heavily biased towards the buffered stable forms that enhance BQS (Figure 8C,D). Additionally, the mode of cross regulation—with transcription factors tending to be either highly regulating or highly regulated (Figure 8F)—also follows the distribution predicted by BQS. Finally, the probability of creating additional long feedback loops in the network by randomly inserting a new regulatory connection is only 0.18, much lower than the value of 0.74 expected in a comparable random network.10.7554/eLife.02863.033Figure 8.BQS in homeostatic murine dendritic cells.
Affiliation: College of Life Sciences, University of Dundee, Dundee, United Kingdom email@example.com.