Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.

Many natural and artificial networks contain overrepresented subgraphs, which have been termed network motifs. In this article, we investigate the processes that led to the formation of the two most common network motifs in eukaryote transcription factor networks: the bi-fan motif and the feed-forwa...

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Autores principales:	Jonathan J Ward, Janet M Thornton
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2007
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/99ef257cc5594c5f91855c24f4925fe9
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spelling	oai:doaj.org-article:99ef257cc5594c5f91855c24f4925fe92021-11-25T05:41:05ZEvolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.1553-734X1553-735810.1371/journal.pcbi.0030198https://doaj.org/article/99ef257cc5594c5f91855c24f4925fe92007-10-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.0030198https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Many natural and artificial networks contain overrepresented subgraphs, which have been termed network motifs. In this article, we investigate the processes that led to the formation of the two most common network motifs in eukaryote transcription factor networks: the bi-fan motif and the feed-forward loop. Around 100 million y ago, the common ancestor of the Saccharomyces clade underwent a whole-genome duplication event. The simultaneous duplication of the genes created by this event enabled the origin of many network motifs to be established. The data suggest that there are two primary mechanisms that are involved in motif formation. The first mechanism, enabled by the substantial plasticity in promoter regions, is rewiring of connections as a result of positive environmental selection. The second is duplication of transcription factors, which is also shown to be involved in the formation of intermediate-scale network modularity. These two evolutionary processes are complementary, with the pre-existence of network motifs enabling duplicated transcription factors to bind different targets despite structural constraints on their DNA-binding specificities. This process may facilitate the creation of novel expression states and the increases in regulatory complexity associated with higher eukaryotes.Jonathan J WardJanet M ThorntonPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 3, Iss 10, Pp 1993-2002 (2007)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jonathan J Ward Janet M Thornton Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
description	Many natural and artificial networks contain overrepresented subgraphs, which have been termed network motifs. In this article, we investigate the processes that led to the formation of the two most common network motifs in eukaryote transcription factor networks: the bi-fan motif and the feed-forward loop. Around 100 million y ago, the common ancestor of the Saccharomyces clade underwent a whole-genome duplication event. The simultaneous duplication of the genes created by this event enabled the origin of many network motifs to be established. The data suggest that there are two primary mechanisms that are involved in motif formation. The first mechanism, enabled by the substantial plasticity in promoter regions, is rewiring of connections as a result of positive environmental selection. The second is duplication of transcription factors, which is also shown to be involved in the formation of intermediate-scale network modularity. These two evolutionary processes are complementary, with the pre-existence of network motifs enabling duplicated transcription factors to bind different targets despite structural constraints on their DNA-binding specificities. This process may facilitate the creation of novel expression states and the increases in regulatory complexity associated with higher eukaryotes.
format	article
author	Jonathan J Ward Janet M Thornton
author_facet	Jonathan J Ward Janet M Thornton
author_sort	Jonathan J Ward
title	Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
title_short	Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
title_full	Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
title_fullStr	Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
title_full_unstemmed	Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.
title_sort	evolutionary models for formation of network motifs and modularity in the saccharomyces transcription factor network.
publisher	Public Library of Science (PLoS)
publishDate	2007
url	https://doaj.org/article/99ef257cc5594c5f91855c24f4925fe9
work_keys_str_mv	AT jonathanjward evolutionarymodelsforformationofnetworkmotifsandmodularityinthesaccharomycestranscriptionfactornetwork AT janetmthornton evolutionarymodelsforformationofnetworkmotifsandmodularityinthesaccharomycestranscriptionfactornetwork
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Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network.

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