Extensive rewiring and complex evolutionary dynamics in a C.elegans multiparameter transcription factor network

John S. Reece-Hoyes; Carles Pons; Alos Diallo; Akihiro Mori; Shaleen Shrestha; Sreenath Kadreppa; Justin Nelson; Stephanie DiPrima; Amelie Dricot; Bryan R. Lajoie; Philippe Souza Moraes Ribeiro; Matthew T. Weirauch; David E. Hill; Timothy R. Hughes; Chad L. Myers; Albertha J.M. Walhout

doi:10.1016/j.molcel.2013.05.018

Extensive rewiring and complex evolutionary dynamics in a C.elegans multiparameter transcription factor network

John S. Reece-Hoyes, Carles Pons, Alos Diallo, Akihiro Mori, Shaleen Shrestha, Sreenath Kadreppa, Justin Nelson, Stephanie DiPrima, Amelie Dricot, Bryan R. Lajoie, Philippe Souza Moraes Ribeiro, Matthew T. Weirauch, David E. Hill, Timothy R. Hughes, Chad L. Myers, Albertha J.M. Walhout

Computer Science and Engineering

Research output: Contribution to journal › Article › peer-review

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Abstract

Gene duplication results in two identical paralogs thatdiverge through mutation, leading to loss or gain of interactions with other biomolecules. Here, we comprehensively characterize such network rewiring for C.elegans transcription factors (TFs) within and across four newly delineated molecular networks. Remarkably, we find that even highly similar TFs often have different interaction degrees and partners. In addition, we find that most TF families have a member that is highly connected in multiple networks. Further, different TF families have opposing correlations between network connectivity and phylogenetic age, suggesting that they are subject to different evolutionary pressures. Finally, TFs that have similar partners in one network generally do not in another, indicating a lack of pressure to retain cross-network similarity. Our multiparameter analyses provide unique insights into the evolutionary dynamics that shaped TF networks.

Original language	English (US)
Pages (from-to)	116-127
Number of pages	12
Journal	Molecular Cell
Volume	51
Issue number	1
DOIs	https://doi.org/10.1016/j.molcel.2013.05.018
State	Published - Jul 11 2013

Bibliographical note

Funding Information:
We thank members of the Walhout and Myers laboratories, J. Dekker, and N. Springer for discussions and critical reading of the manuscript. This work was supported by National Institutes of Health (NIH) grant GM082971 to A.J.M.W. and D.E.H.; NIH grant DK06429 to A.J.M.W.; CIHR grant MOP-111007 to T.R.H.; fellowships from CIHR and CIFAR to M.T.W.; and C.L.M., C.P., J.N., and P.S.M.R. are partially supported by grants from the NIH (HG005084-01A1, HG005853-01) and the National Science Foundation (DBI 0953881).

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Reece-Hoyes, J. S., Pons, C., Diallo, A., Mori, A., Shrestha, S., Kadreppa, S., Nelson, J., DiPrima, S., Dricot, A., Lajoie, B. R., Ribeiro, P. S. M., Weirauch, M. T., Hill, D. E., Hughes, T. R., Myers, C. L., & Walhout, A. J. M. (2013). Extensive rewiring and complex evolutionary dynamics in a C.elegans multiparameter transcription factor network. Molecular Cell, 51(1), 116-127. https://doi.org/10.1016/j.molcel.2013.05.018

Reece-Hoyes, JS, Pons, C, Diallo, A, Mori, A, Shrestha, S, Kadreppa, S, Nelson, J, DiPrima, S, Dricot, A, Lajoie, BR, Ribeiro, PSM, Weirauch, MT, Hill, DE, Hughes, TR, Myers, CL & Walhout, AJM 2013, 'Extensive rewiring and complex evolutionary dynamics in a C.elegans multiparameter transcription factor network', Molecular Cell, vol. 51, no. 1, pp. 116-127. https://doi.org/10.1016/j.molcel.2013.05.018

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abstract = "Gene duplication results in two identical paralogs thatdiverge through mutation, leading to loss or gain of interactions with other biomolecules. Here, we comprehensively characterize such network rewiring for C.elegans transcription factors (TFs) within and across four newly delineated molecular networks. Remarkably, we find that even highly similar TFs often have different interaction degrees and partners. In addition, we find that most TF families have a member that is highly connected in multiple networks. Further, different TF families have opposing correlations between network connectivity and phylogenetic age, suggesting that they are subject to different evolutionary pressures. Finally, TFs that have similar partners in one network generally do not in another, indicating a lack of pressure to retain cross-network similarity. Our multiparameter analyses provide unique insights into the evolutionary dynamics that shaped TF networks.",

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Extensive rewiring and complex evolutionary dynamics in a C.elegans multiparameter transcription factor network

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