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Cells
Special Issues
Crossroads between Gene Regulatory Networks and Evolution
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Crossroads between Gene Regulatory Networks and Evolution

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Cell and Gene Therapy".

Deadline for manuscript submissions: closed (25 March 2023) | Viewed by 9320

Special Issue Editors

Dr. Maria Ina Arnone

E-Mail Website
Guest Editor
Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
Interests: Gene Regulatory Networks (GRN); evolution of organs and body parts; developmental biology; gut patterning; vision; echinoderm; sea urchin
Prof. Paola Oliveri

E-Mail Website
Guest Editor
Department of Genetics, Evolution & Environment, University College London, London WC1E 6BT, UK
Interests: evolution of development; Gene Regulatory Networks; regeneration; cell type specification; skeleton; neuropeptides
Dr. Roberto Feuda

E-Mail Website
Guest Editor
Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
Interests: gene regulatory networks (GRNs); phylogenomics; evo-devo

Special Issue Information

Dear Colleagues,

Gene regulatory networks (GRNs) explain how genetic information controls various aspects of living systems, from development to behaviour; however, their evolution remains poorly understood. While traditionally limited to a few model systems, the recent development of molecular (e.g., single-cell technology and CRISPR) and computational methods has opened the opportunity to investigate GRNs controlling the different levels of biological organisation in a multitude of organisms at an unprecedented level of resolution. These technical developments, combined with the definition of a unified language, will open the opportunity to understand general and common rules governing evolution GRNs.

This Special Issue aims to synthesise the current field of GRNs in different organisms and to add breakthrough findings that could improve our understanding of GRN evolution. We are looking for original research and review articles that will contribute to understanding the evolution of GRNs at a different level of biological organisation from gene circuits to cells, organs, and organisms.

This Special Issue will focus on developing common language and tools to investigate the evolution of GRNs in living forms, providing, ultimately, general principles that can be used to rewrite cell fate and design synthetic circuits.

Dr. Maria Ina Arnone
Prof. Paola Oliveri
Dr. Roberto Feuda
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Gene regulatory network
  • Development
  • Evolution
  • Cis-regulatory element
  • Transcriptional control
  • synthetic circuit
  • Regulatory module
  • Regulatory logic
  • Cell type

Published Papers (3 papers)

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Review

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23 pages, 5533 KiB  
Review
The Evolution of Biomineralization through the Co-Option of Organic Scaffold Forming Networks
by Smadar Ben-Tabou de-Leon
Cells 2022, 11(4), 595; https://doi.org/10.3390/cells11040595 - 9 Feb 2022
Cited by 11 | Viewed by 3249
Abstract
Biomineralization is the process in which organisms use minerals to generate hard structures like teeth, skeletons and shells. Biomineralization is proposed to have evolved independently in different phyla through the co-option of pre-existing developmental programs. Comparing the gene regulatory networks (GRNs) that drive [...] Read more.
Biomineralization is the process in which organisms use minerals to generate hard structures like teeth, skeletons and shells. Biomineralization is proposed to have evolved independently in different phyla through the co-option of pre-existing developmental programs. Comparing the gene regulatory networks (GRNs) that drive biomineralization in different species could illuminate the molecular evolution of biomineralization. Skeletogenesis in the sea urchin embryo was extensively studied and the underlying GRN shows high conservation within echinoderms, larval and adult skeletogenesis. The organic scaffold in which the calcite skeletal elements form in echinoderms is a tubular compartment generated by the syncytial skeletogenic cells. This is strictly different than the organic cartilaginous scaffold that vertebrates mineralize with hydroxyapatite to make their bones. Here I compare the GRNs that drive biomineralization and tubulogenesis in echinoderms and in vertebrates. The GRN that drives skeletogenesis in the sea urchin embryo shows little similarity to the GRN that drives bone formation and high resemblance to the GRN that drives vertebrates’ vascular tubulogenesis. On the other hand, vertebrates’ bone-GRNs show high similarity to the GRNs that operate in the cells that generate the cartilage-like tissues of basal chordate and invertebrates that do not produce mineralized tissue. These comparisons suggest that biomineralization in deuterostomes evolved through the phylum specific co-option of GRNs that control distinct organic scaffolds to mineralization. Full article
(This article belongs to the Special Issue Crossroads between Gene Regulatory Networks and Evolution)
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13 pages, 1382 KiB  
Review
Common Themes and Future Challenges in Understanding Gene Regulatory Network Evolution
by Isabella Schember and Marc S. Halfon
Cells 2022, 11(3), 510; https://doi.org/10.3390/cells11030510 - 1 Feb 2022
Cited by 5 | Viewed by 2851
Abstract
A major driving force behind the evolution of species-specific traits and novel structures is alterations in gene regulatory networks (GRNs). Comprehending evolution therefore requires an understanding of the nature of changes in GRN structure and the responsible mechanisms. Here, we review two insect [...] Read more.
A major driving force behind the evolution of species-specific traits and novel structures is alterations in gene regulatory networks (GRNs). Comprehending evolution therefore requires an understanding of the nature of changes in GRN structure and the responsible mechanisms. Here, we review two insect pigmentation GRNs in order to examine common themes in GRN evolution and to reveal some of the challenges associated with investigating changes in GRNs across different evolutionary distances at the molecular level. The pigmentation GRN in Drosophila melanogaster and other drosophilids is a well-defined network for which studies from closely related species illuminate the different ways co-option of regulators can occur. The pigmentation GRN for butterflies of the Heliconius species group is less fully detailed but it is emerging as a useful model for exploring important questions about redundancy and modularity in cis-regulatory systems. Both GRNs serve to highlight the ways in which redeployment of trans-acting factors can lead to GRN rewiring and network co-option. To gain insight into GRN evolution, we discuss the importance of defining GRN architecture at multiple levels both within and between species and of utilizing a range of complementary approaches. Full article
(This article belongs to the Special Issue Crossroads between Gene Regulatory Networks and Evolution)
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Other

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16 pages, 661 KiB  
Perspective
Spatially and Temporally Distributed Complexity—A Refreshed Framework for the Study of GRN Evolution
by Alessandro Minelli and Alberto Valero-Gracia
Cells 2022, 11(11), 1790; https://doi.org/10.3390/cells11111790 - 30 May 2022
Cited by 2 | Viewed by 2201
Abstract
Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a [...] Read more.
Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a putatively hierarchical organization of animal body plans. Here, we constructively criticize these assumptions. First, developmental biology is pervaded by adultocentrism, but development is not necessarily egg to adult. Second, during development, many unicells undergo transcriptomic profile transitions that are comparable to those recorded in pluricellular organisms; thus, their study should not be neglected from the GRN perspective. Third, the putatively hierarchical nature of the animal body is mirrored in the GRN logic, but in relating genotype to phenotype, independent assessments of the dynamics of the regulatory machinery and the animal’s architecture are required, better served by a combinatorial than by a hierarchical approach. The trade-offs between spatial and temporal aspects of regulation, as well as their evolutionary consequences, are also discussed. Multicellularity may derive from a unicell’s sequential phenotypes turned into different but coexisting, spatially arranged cell types. In turn, polyphenism may have been a crucial mechanism involved in the origin of complex life cycles. Full article
(This article belongs to the Special Issue Crossroads between Gene Regulatory Networks and Evolution)
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