Putting transcriptional network evolution at the heart of evolutionary biology. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution. (2006). Eric H. Davidson. Academic Press, San Diego. Xi + 289 pp. ISBN 978-0-12-088563-3

BioEssays ◽  
2007 ◽  
Vol 29 (11) ◽  
pp. 1175-1177
Author(s):  
Adam S. Wilkins
Keyword(s):  
Gene Regulatory Networks ◽  
Evolutionary Biology ◽  
San Diego ◽  
Regulatory Networks ◽  
Network Evolution ◽  
Transcriptional Network ◽  
Academic Press ◽  
Regulatory Genome ◽  
Gene Regulatory ◽  
Development And Evolution

scholarly journals Compensatory mutation can drive gene regulatory network evolution

2019 ◽  
Author(s):  
Yifei Wang ◽  
Marios Richards ◽  
Steve Dorus ◽  
Nicholas K. Priest ◽  
Joanna J. Bryson
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Network Evolution ◽  
Regulatory Function ◽  
Compensatory Mutation ◽  
Relaxed Selection ◽  
Mutation Site ◽  
Regulatory Pathways ◽  
Gene Regulatory

AbstractGene regulatory networks underlie every aspect of life; better understanding their assembly would better our understanding of evolution more generally. For example, evolutionary theory typically assumed that low-fitness intermediary pathways are not a significant factor in evolution, yet there is substantial empirical evidence of compensatory mutation. Here we revise theoretical assumptions to explore the possibility that compensatory mutation may drive rapid evolutionary recovery. Using a well-established in silico model of gene regulatory networks, we show that assuming only that deleterious mutations are not fatal, compensatory mutation is surprisingly frequent. Further, we find that it entails biases that drive the evolution of regulatory pathways. In our simulations, we find compensatory mutation to be common during periods of relaxed selection, with 8-15% of degraded networks having regulatory function restored by a single randomly-generated additional mutation. Though this process reduces average robustness, proportionally higher robustness is found in networks where compensatory mutations occur close to the deleterious mutation site, or where the compensatory mutation results in a large regulatory effect size. This location- and size-specific robustness systematically biases which networks are purged by selection for network stability, producing emergent changes to the population of regulatory networks. We show that over time, large-effect and co-located mutations accumulate, assuming only that episodes of relaxed selection occur, even very rarely. This accumulation results in an increase in regulatory complexity. Our findings help explain a process by which large-effect mutations structure complex regulatory networks, and may account for the speed and pervasiveness of observed occurrence of compensatory mutation, for example in the context of antibiotic resistance, which we discuss. If sustained by in vitro experiments, these results promise a significant breakthrough in the understanding of evolutionary and regulatory processes.

scholarly journals Phase transitions and assortativity in models of gene regulatory networks evolved under different selection processes

2021 ◽  
Vol 18 (177) ◽  
Author(s):  
Brandon Alexander ◽  
Alexandra Pushkar ◽  
Michelle Girvan
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Large Scale ◽  
Target Genes ◽  
Network Evolution ◽  
Network Nodes ◽  
Individual Gene ◽  
Damage Propagation ◽  
Selection Processes ◽  
Gene Regulatory

We study a simplified model of gene regulatory network evolution in which links (regulatory interactions) are added via various selection rules that are based on the structural and dynamical features of the network nodes (genes). Similar to well-studied models of ‘explosive’ percolation, in our approach, links are selectively added so as to delay the transition to large-scale damage propagation, i.e. to make the network robust to small perturbations of gene states. We find that when selection depends only on structure, evolved networks are resistant to widespread damage propagation, even without knowledge of individual gene propensities for becoming ‘damaged’. We also observe that networks evolved to avoid damage propagation tend towards disassortativity (i.e. directed links preferentially connect high degree ‘source’ genes to low degree ‘target’ genes and vice versa). We compare our simulations to reconstructed gene regulatory networks for several different species, with genes and links added over evolutionary time, and we find a similar bias towards disassortativity in the reconstructed networks.

scholarly journals An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia

2019 ◽  
Author(s):  
Ben J. Vincent ◽  
Gavin R. Rice ◽  
Gabriella M. Wong ◽  
William J. Glassford ◽  
Kayla I. Downs ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transcription Factors ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Rna Seq ◽  
Pupal Development ◽  
Searchable Database ◽  
Gene Regulatory ◽  
Development And Evolution

AbstractDuring development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mapping transcription factor landscapes is important, especially in tissues that undergo rapid evolutionary change. The terminalia (genital and anal structures) of Drosophila melanogaster and its close relatives exhibit dramatic changes in morphology between species. While previous studies have found network components important for patterning the larval genital disc, the networks governing adult structures during pupal development have remained uncharted. Here, we performed RNA-seq in whole Drosophila melanogaster terminalia followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the terminalia is highly patterned during pupal stages and that specific transcription factors mark separate structures and substructures. Our results are housed online in a searchable database (flyterminalia.pitt.edu) where they can serve as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.SummaryWe performed RNA-seq in whole Drosophila melanogaster terminalia (genitalia and analia) followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the pupal terminalia is highly patterned with specific transcription factors marking separate structures and substructures. Our results are housed online in a searchable database (flyterminalia.pitt.edu) where they can serve as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.

scholarly journals Evolving Views on the Pallium

2021 ◽  
pp. 1-19
Author(s):  
Loreta Medina ◽  
Antonio Abellán ◽  
Ester Desfilis
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Double Ring ◽  
Neural Populations ◽  
Research Questions ◽  
Gene Regulatory ◽  
Architecture Development ◽  
Activity Dependent ◽  
Organizing Principles ◽  
Development And Evolution

The pallium is the largest part of the telencephalon in amniotes, and comparison of its subdivisions across species has been extremely difficult and controversial due to its high divergence. Comparative embryonic genoarchitecture studies have greatly contributed to propose models of pallial fundamental divisions, which can be compared across species and be used to extract general organizing principles as well as to ask more focused and insightful research questions. The use of these models is crucial to discern between conservation, convergence or divergence in the neural populations and networks found in the pallium. Here we provide a critical review of the models proposed using this approach, including tetrapartite, hexapartite and double-ring models, and compare them to other models. While recognizing the power of these models for understanding brain architecture, development and evolution, we also highlight limitations and comment on aspects that require attention for improvement. We also discuss on the use of transcriptomic data for understanding pallial evolution and advise for better contextualization of these data by discerning between gene regulatory networks involved in the generation of specific units and cell populations versus genes expressed later, many of which are activity dependent and their expression is more likely subjected to convergent evolution.

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