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Sci. Signal., 2 November 2010
Vol. 3, Issue 146, p. ra79
[DOI: 10.1126/scisignal.2001014]

RESEARCH ARTICLES

Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators

Nitin Bhardwaj1, Philip M. Kim2,3,4,5*, and Mark B. Gerstein1,6,7*

1 Program in Computational Biology and Bioinformatics, Yale University, Bass 426, 266 Whitney Avenue, New Haven, CT 06520, USA.
2 Terrence Donnelly Centre for Cellular and Biomolecular Research, Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.
3 Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.
4 Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1.
5 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 3E1.
6 Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.
7 Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

Abstract: Network connectivity has been related to essentiality: Highly connected proteins (hubs) are more important for cell growth and survival. Although this is intuitively reasonable, another way to assess the role of a regulator is to assign it to a level within a "chain-of-command" hierarchy. Here, we analyzed the effects of network rewiring events on transcriptional regulatory hierarchies in two species. First, we superimposed the phenotypic effects of tampering with specific genes and their regulatory connections directly onto the hierarchies. To study second-order effects, which involved changes in the level of regulators within the hierarchy upon deletions or insertions of other regulators or connections, we reconstructed modified hierarchies. We found that rewiring events that affected upper levels had a more marked effect on cell proliferation rate and survival than did those involving lower levels. Moreover, we showed that the hierarchical level and type of change better reflected the phenotypic effect of rewiring than did the number of changes. We also investigated other features connected to the importance of upper-level regulators: In particular, relative to lower-level regulators, upper-level regulators exhibited a greater range of expression values across species, had fewer functionally redundant copies, and had a shorter half-life. Overall, our analysis shows that broadly constructed hierarchies may better reflect the importance of regulators for cell growth than classifications based on the number of connections (hubbiness).

* To whom correspondence should be addressed. E-mail: pi{at}kimlab.org (P.M.K.); mark.gerstein{at}yale.edu (M.B.G.)

Citation: N. Bhardwaj, P. M. Kim, M. B. Gerstein, Rewiring of Transcriptional Regulatory Networks: Hierarchy, Rather Than Connectivity, Better Reflects the Importance of Regulators. Sci. Signal. 3, ra79 (2010).

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THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
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The co-regulation mechanism of transcription factors in the human gene regulatory network.
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