The Evolution of Transcriptional Regulation in Eukaryotes

Wray, Gregory A.; Hahn, Matthew W.; Abouheif, Ehab; Balhoff, James P.; Pizer, Margaret; Rockman, Matthew V.; Romanò, Laura

doi:10.1093/molbev/msg140

Cited by 1,052 publications

(892 citation statements)

References 398 publications

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“…On the one hand, regulatory interactions are often mediated by very short amino acid and DNA sequences, for example in transcriptional regulation or protein phosphorylation [62][63][64][65][66]. Such short sequences can evolve rapidly and might endow regulatory circuits with flexible, almost unconstrained phenotypes.…”

Section: Physicochemical Constraintsmentioning

confidence: 99%

Genotype networks shed light on evolutionary constraints

Wagner

2011

Trends in Ecology & Evolution

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An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. One can distinguish physicochemical, selective, genetic and developmental causes of such constraints. Here, I discuss these causes in three classes of system that bring forth many phenotypic traits and evolutionary innovations: regulatory circuits, macromolecules and metabolic networks. In these systems, genotypes with the same phenotype form large genotype networks that extend throughout a vast genotype space. Such genotype networks can help unify different causes of evolutionary constraints. They can show that these causes ultimately emerge from the process of development; that is, how phenotypes form from genotypes. Furthermore, they can explain important consequences of constraints, such as punctuated stasis and canalization. An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. One can distinguish physicochemical, selective, genetic and developmental causes of such constraints. Here, I discuss these causes in three classes of systems that bring forth many phenotypic traits and evolutionary innovations: regulatory circuits, macromolecules and metabolic networks. In these systems, genotypes with the same phenotype form large genotype networks that extend throughout a vast genotype space. Such genotype networks can help unify different causes of evolutionary constraints. They can show that these causes ultimately emerge from the process of development: that is, how phenotypes form from genotypes. Furthermore, they can explain important consequences of constraints, such as punctuated stasis and canalization. Evolutionary constraintsNo organism or species can produce every conceivable kind of phenotypic variation. This limitation is encapsulated in the notion of constraints on phenotypic evolution [1]. An evolutionary constraint is a bias or limitation in phenotypic variation that a biological system produces. Extreme examples include the absence of photosynthesis in higher animals, the general lack of teeth in the lower jaw of frogs, the absence of palm trees in cold climates and the absence of birds that give birth to live young instead of to eggs [1,2]. In these examples, a trait is completely absent. More subtle constraints manifest themselves as correlations among different characters. A paradigmatic case is allometric scaling [2]. Here, the value of one quantitative trait constrains that of another, typically via a specific nonlinear relationship, For example, metabolic rate is proportional to body mass m raised to approximately three quarter power (m 0.75 ) across many differentIt is not hard to see that constraints can influence the spectrum of evolutionary adaptations and innovations that are accessible to living things. For this reason, questions about the causes and consequences of constrained evolution have attracted much attention [1,[4][5][6][7][8][9][10]. There are multiple kinds and causes of phenotypic constraints (Box 1),...

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Section: Physicochemical Constraintsmentioning

confidence: 99%

Genotype networks shed light on evolutionary constraints

Wagner

2011

Trends in Ecology & Evolution

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“…Transcription factors (TFs) are types of proteins that regulate gene expression by binding to specific cis-acting promoter elements, thereby activating or repressing the transcriptional rates of their target genes [1,2]. Thus, the identification and functional characterization of TFs is essential for the reconstruction of transcriptional regulatory networks [3].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

et al. 2010

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BackgroundNAC (NAM, ATAF1/2 and CUC2) domain proteins are plant-specific transcriptional factors known to play diverse roles in various plant developmental processes. NAC transcription factors comprise of a large gene family represented by more than 100 members in Arabidopsis, rice and soybean etc. Recently, a preliminary phylogenetic analysis was reported for NAC gene family from 11 plant species. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, conserved motifs, and expression profiling analysis has been presented thus far for the model tree species Populus.ResultsIn the present study, a comprehensive analysis of NAC gene family in Populus was performed. A total of 163 full-length NAC genes were identified in Populus, and they were phylogeneticly clustered into 18 distinct subfamilies. The gene structure and motif compositions were considerably conserved among the subfamilies. The distributions of 120 Populus NAC genes were non-random across the 19 linkage groups (LGs), and 87 genes (73%) were preferentially retained duplicates that located in both duplicated regions. The majority of NACs showed specific temporal and spatial expression patterns based on EST frequency and microarray data analyses. However, the expression patterns of a majority of duplicate genes were partially redundant, suggesting the occurrence of subfunctionalization during subsequent evolutionary process. Furthermore, quantitative real-time RT-PCR (RT-qPCR) was performed to confirm the tissue-specific expression patterns of 25 NAC genes.ConclusionBased on the genomic organizations, we can conclude that segmental duplications contribute significantly to the expansion of Populus NAC gene family. The comprehensive expression profiles analysis provides first insights into the functional divergence among members in NAC gene family. In addition, the high divergence rate of expression patterns after segmental duplications indicates that NAC genes in Populus are likewise to have been retained by substantial subfunctionalization. Taken together, our results presented here would be helpful in laying the foundation for functional characterization of NAC gene family and further gaining an understanding of the structure-function relationship between these family members.

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“…One possible explanation is that decaying TE sequences provide materials from which cis-regulatory elements can be constructed de novo through the introduction of single or a few point mutations (Feschotte, 2008) because most transcription factor binding sites consist of short degenerate sequences (Wray et al, 2003). Two other possibilities are that cisregulatory elements are already present within the TE at the time of its insertion and are co-opted immediately upon insertion or after modifications in the surrounding environment (Feschotte, 2008) or that its "pre-sites" only require a few mutations to originate functional TFBSs (de Souza et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

Carareto

Hernandez

Vieira

2014

Gene

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a b s t r a c tIn the present study, an in silico analysis was performed to identify transposable element (TE) fragments inserted in Cyps with functions associated with resistance to insecticides and developmental regulation as well as in neighboring genes in two sibling species , Drosophila melanogaster and Drosophila simulans . The Cyps associated with insecticide resistance and their neighboring non-Cyp genes have accumulated a greater number of TE fragments than the other Cyps or a random sample of genes, predominantly in the 5′-flanking regions. Most of the insertions were due to DNA transposons, with DNAREP1 fragments being the most common. These fragments carry putative binding sites for transcription factors, which reinforces the hypothesis that DNAREP1 may influence gene regulation and play a role in the adaptation of the Drosophila species.

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The Evolution of Transcriptional Regulation in Eukaryotes

Cited by 1,052 publications

References 398 publications

Genotype networks shed light on evolutionary constraints

Genotype networks shed light on evolutionary constraints

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

Genomic regions harboring insecticide resistance-associated Cyp genes are enriched by transposable element fragments carrying putative transcription factor binding sites in two sibling Drosophila species

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