How Transcription Networks Evolve and Produce Biological Novelty

Nocedal, Isabel; Johnson, Alexander D.

doi:10.1101/sqb.2015.80.027557

Cited by 26 publications

(24 citation statements)

References 70 publications

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“…While transcriptional networks can undergo rapid rewiring at the level of enhancer binding sites during yeast, insect and mammalian evolution [54,55], the direct transcriptional targets of Lef1 mediating hypothalamic neurogenesis are still unknown. We have identified Tcf/Lef consensus binding sites in zebrafish and mouse Crhbp and Pmch loci, but it remains important to determine whether these 2 genes are direct targets of Lef1, or are instead lost as a secondary result of neurogenesis defects in mutants.…”

Section: Discussionmentioning

confidence: 99%

Lef1-dependent hypothalamic neurogenesis inhibits anxiety

et al. 2017

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While innate behaviors are conserved throughout the animal kingdom, it is unknown whether common signaling pathways regulate the development of neuronal populations mediating these behaviors in diverse organisms. Here, we demonstrate that the Wnt/ß-catenin effector Lef1 is required for the differentiation of anxiolytic hypothalamic neurons in zebrafish and mice, although the identity of Lef1-dependent genes and neurons differ between these 2 species. We further show that zebrafish and Drosophila have common Lef1-dependent gene expression in their respective neuroendocrine organs, consistent with a conserved pathway that has diverged in the mouse. Finally, orthologs of Lef1-dependent genes from both zebrafish and mouse show highly correlated hypothalamic expression in marmosets and humans, suggesting co-regulation of 2 parallel anxiolytic pathways in primates. These findings demonstrate that during evolution, a transcription factor can act through multiple mechanisms to generate a common behavioral output, and that Lef1 regulates circuit development that is fundamentally important for mediating anxiety in a wide variety of animal species.

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Section: Discussionmentioning

confidence: 99%

Lef1-dependent hypothalamic neurogenesis inhibits anxiety

et al. 2017

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“…Rewiring of gene regulatory networks is an important mechanism of evolutionary adaptation [75]. It has, for example, recently been shown that the zinc cluster protein Ppr1 regulates pyrimidine biosynthesis in budding yeast but allantoin catabolism in C .…”

Section: Orthologs Of Ecm22 Upc2 Sut1 and Sut2 In Other Speciesmentioning

confidence: 99%

From Lipid Homeostasis to Differentiation: Old and New Functions of the Zinc Cluster Proteins Ecm22, Upc2, Sut1 and Sut2

Joshua

Höfken

2017

IJMS

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Zinc cluster proteins are a large family of transcriptional regulators with a wide range of biological functions. The zinc cluster proteins Ecm22, Upc2, Sut1 and Sut2 have initially been identified as regulators of sterol import in the budding yeast Saccharomyces cerevisiae. These proteins also control adaptations to anaerobic growth, sterol biosynthesis as well as filamentation and mating. Orthologs of these zinc cluster proteins have been identified in several species of Candida. Upc2 plays a critical role in antifungal resistance in these important human fungal pathogens. Upc2 is therefore an interesting potential target for novel antifungals. In this review we discuss the functions, mode of actions and regulation of Ecm22, Upc2, Sut1 and Sut2 in budding yeast and Candida.

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“…Nocedal and Johnson [7] write “We do not yet understand how a large network, composed of many transcription regulators and hundreds or thousands of target genes, forms in the first place.” We believe that considering only cases in which one transcription factor is switched with another will be inadequate to describe the evolution of networks. They also write “A change even in the regulation of a single gene can have important consequences in modern species’....…”

Section: Resultsmentioning

confidence: 99%

“…A motif is a short segment in the DNA sequence, between 6–20 nucleotide pairs, usually fewer than 10, that can be positioned at different locations within the regulatory region of a gene [7]. Tanay et al [8] focus on identifying motifs that are “enriched”, i.e., the motif occurs in multiple species, controlling analogous regulons in those species.…”

Section: Introductionmentioning

confidence: 99%

“…Nocedal and Johnson [7] analyze more complex cases of transcription factor rewiring in yeast and concludes that future research is needed to understand transcription factor rewiring in regulatory networks that involve multiple transcription factors and larger regulons . They also say that it is important to consider evolution in the study of transcription factor rewiring.…”

Section: Introductionmentioning

confidence: 99%

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Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species

Muñoz

Zimin

et al. 2016

BMC Genomics

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BackgroundThe diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species.ResultsWe have created a method (based on our new “ping-pong algorithm) for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes. An example is illustrative. A rewiring has been reported by Hogues et al. that RAP1 in Saccharomyces cerevisiae substitutes for TBF1/CBF1 in Candida albicans for ribosomal RP genes. There one transcription factor substitutes for another on some collection of genes. Such a substitution is referred to as a “rewiring”. We agree with this finding of rewiring as far as it goes but the situation is more complicated. Many transcription factors can regulate a gene and our algorithm finds that in this example a “team” (or collection) of three transcription factors including RAP1 substitutes for TBF1 for 19 genes. The switch occurs for a branch of the phylogenetic tree containing 10 species (including Saccharomyces cerevisiae), while the remaining 13 species (Candida albicans) are regulated by TBF1.ConclusionsTo gain insight into more general evolutionary mechanisms, we have created a mathematical algorithm that finds such general switching events and we prove that it converges. Of course any such computational discovery should be validated in the biological tests. For each branch of the phylogenetic tree and each gene module, our algorithm finds a sub-group of co-regulated genes and a team of transcription factors that substitutes for another team of transcription factors. In most cases the signal will be small but in some cases we find a strong signal of switching. We report our findings for 23 Ascomycota fungi species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3102-7) contains supplementary material, which is available to authorized users.

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How Transcription Networks Evolve and Produce Biological Novelty

Cited by 26 publications

References 70 publications

Lef1-dependent hypothalamic neurogenesis inhibits anxiety

Lef1-dependent hypothalamic neurogenesis inhibits anxiety

From Lipid Homeostasis to Differentiation: Old and New Functions of the Zinc Cluster Proteins Ecm22, Upc2, Sut1 and Sut2

Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species

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