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Evodevo
2023 Jun 16;141:10. doi: 10.1186/s13227-023-00214-y.
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Feedback circuits are numerous in embryonic gene regulatory networks and offer a stabilizing influence on evolution of those networks.
Massri AJ
,
McDonald B
,
Wray GA
,
McClay DR
.
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The developmental gene regulatory networks (dGRNs) of two sea urchin species, Lytechinus variegatus (Lv) and Strongylocentrotus purpuratus (Sp), have remained remarkably similar despite about 50 million years since a common ancestor. Hundreds of parallel experimental perturbations of transcription factors with similar outcomes support this conclusion. A recent scRNA-seq analysis suggested that the earliest expression of several genes within the dGRNs differs between Lv and Sp. Here, we present a careful reanalysis of the dGRNs in these two species, paying close attention to timing of first expression. We find that initial expression of genes critical for cell fate specification occurs during several compressed time periods in both species. Previously unrecognized feedback circuits are inferred from the temporally corrected dGRNs. Although many of these feedbacks differ in location within the respective GRNs, the overall number is similar between species. We identify several prominent differences in timing of first expression for key developmental regulatory genes; comparison with a third species indicates that these heterochronies likely originated in an unbiased manner with respect to embryonic cell lineage and evolutionary branch. Together, these results suggest that interactions can evolve even within highly conserved dGRNs and that feedback circuits may buffer the effects of heterochronies in the expression of key regulatory genes.
Ben-Tabou de-Leon,
Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown.
2013, Pubmed,
Echinobase
Ben-Tabou de-Leon,
Gene regulatory control in the sea urchin aboral ectoderm: spatial initiation, signaling inputs, and cell fate lockdown.
2013,
Pubmed
,
Echinobase
Bessodes,
Reciprocal signaling between the ectoderm and a mesendodermal left-right organizer directs left-right determination in the sea urchin embryo.
2012,
Pubmed
,
Echinobase
Bolouri,
Transcriptional regulatory cascades in development: initial rates, not steady state, determine network kinetics.
2003,
Pubmed
,
Echinobase
Brandman,
Feedback loops shape cellular signals in space and time.
2008,
Pubmed
Brandman,
Interlinked fast and slow positive feedback loops drive reliable cell decisions.
2005,
Pubmed
Cary,
Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development.
2020,
Pubmed
,
Echinobase
Croce,
A genome-wide survey of the evolutionarily conserved Wnt pathways in the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Croce,
Dynamics of Delta/Notch signaling on endomesoderm segregation in the sea urchin embryo.
2010,
Pubmed
,
Echinobase
Davidson,
Network design principles from the sea urchin embryo.
2009,
Pubmed
,
Echinobase
Davidson,
A comparative analysis of egg provisioning using mass spectrometry during rapid life history evolution in sea urchins.
2019,
Pubmed
,
Echinobase
Davidson,
A genomic regulatory network for development.
2002,
Pubmed
,
Echinobase
Davidson,
Gene regulatory networks and the evolution of animal body plans.
2006,
Pubmed
Duboc,
Nodal and BMP2/4 signaling organizes the oral-aboral axis of the sea urchin embryo.
2004,
Pubmed
,
Echinobase
Duboc,
Nodal and BMP2/4 pattern the mesoderm and endoderm during development of the sea urchin embryo.
2010,
Pubmed
,
Echinobase
Ebert,
Longevity and lack of senescence in the red sea urchin Strongylocentrotus franciscanus.
2008,
Pubmed
,
Echinobase
El-Samad,
Biological feedback control-Respect the loops.
2021,
Pubmed
Elowitz,
A synthetic oscillatory network of transcriptional regulators.
2000,
Pubmed
Erkenbrack,
Evolutionary rewiring of gene regulatory network linkages at divergence of the echinoid subclasses.
2015,
Pubmed
,
Echinobase
Erwin,
The evolution of hierarchical gene regulatory networks.
2009,
Pubmed
Gildor,
Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics.
2015,
Pubmed
,
Echinobase
Gildor,
Regulatory heterochronies and loose temporal scaling between sea star and sea urchin regulatory circuits.
2017,
Pubmed
,
Echinobase
Henninger,
RNA-Mediated Feedback Control of Transcriptional Condensates.
2021,
Pubmed
Hines,
Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation.
2012,
Pubmed
Hinman,
Evolutionary plasticity of developmental gene regulatory network architecture.
2007,
Pubmed
,
Echinobase
Howard-Ashby,
Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development.
2006,
Pubmed
,
Echinobase
Howard-Ashby,
Gene families encoding transcription factors expressed in early development of Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Israel,
Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris.
2016,
Pubmed
,
Echinobase
Lapraz,
RTK and TGF-beta signaling pathways genes in the sea urchin genome.
2006,
Pubmed
,
Echinobase
Li,
Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo.
2012,
Pubmed
,
Echinobase
Li,
New regulatory circuit controlling spatial and temporal gene expression in the sea urchin embryo oral ectoderm GRN.
2013,
Pubmed
,
Echinobase
Li,
Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo.
2014,
Pubmed
,
Echinobase
Longabaugh,
Visualization, documentation, analysis, and communication of large-scale gene regulatory networks.
2009,
Pubmed
Love,
Gene expression patterns in a novel animal appendage: the sea urchin pluteus arm.
2007,
Pubmed
,
Echinobase
Love,
Co-option and dissociation in larval origins and evolution: the sea urchin larval gut.
2008,
Pubmed
,
Echinobase
Lyons,
Morphogenesis in sea urchin embryos: linking cellular events to gene regulatory network states.
2012,
Pubmed
,
Echinobase
Mallarino,
Developmental mechanisms of stripe patterns in rodents.
2016,
Pubmed
Martik,
Developmental gene regulatory networks in sea urchins and what we can learn from them.
2016,
Pubmed
,
Echinobase
Martik,
New insights from a high-resolution look at gastrulation in the sea urchin, Lytechinus variegatus.
2017,
Pubmed
,
Echinobase
Massri,
Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo.
2021,
Pubmed
,
Echinobase
Materna,
The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development.
2006,
Pubmed
,
Echinobase
Materna,
High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development.
2010,
Pubmed
,
Echinobase
Morris,
Early development of the feeding larva of the sea urchin Heliocidaris tuberculata: role of the small micromeres.
2019,
Pubmed
,
Echinobase
Nielsen,
Novel gene expression patterns in hybrid embryos between species with different modes of development.
2000,
Pubmed
,
Echinobase
Peter,
A gene regulatory network controlling the embryonic specification of endoderm.
2011,
Pubmed
,
Echinobase
Peter,
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.
2010,
Pubmed
,
Echinobase
Saudemont,
Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm.
2010,
Pubmed
,
Echinobase
Saunders,
Sub-circuits of a gene regulatory network control a developmental epithelial-mesenchymal transition.
2014,
Pubmed
,
Echinobase
Schiebinger,
Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming.
2019,
Pubmed
Su,
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo.
2009,
Pubmed
,
Echinobase
Tishkoff,
Convergent adaptation of human lactase persistence in Africa and Europe.
2007,
Pubmed
Tu,
Sea urchin Forkhead gene family: phylogeny and embryonic expression.
2006,
Pubmed
,
Echinobase
Walton,
Genomics and expression profiles of the Hedgehog and Notch signaling pathways in sea urchin development.
2006,
Pubmed
,
Echinobase
Wang,
Genetic basis for divergence in developmental gene expression in two closely related sea urchins.
2020,
Pubmed
,
Echinobase
Wilson,
Dissociation of expression patterns of homeodomain transcription factors in the evolution of developmental mode in the sea urchins Heliocidaris tuberculata and H. erythrogramma.
2005,
Pubmed
,
Echinobase
Wittkopp,
Drosophila pigmentation evolution: divergent genotypes underlying convergent phenotypes.
2003,
Pubmed
Wray,
Extreme phenotypic divergence and the evolution of development.
2022,
Pubmed
,
Echinobase
Wray,
MOLECULAR HETEROCHRONIES AND HETEROTOPIES IN EARLY ECHINOID DEVELOPMENT.
1989,
Pubmed
Wu,
The Snail repressor is required for PMC ingression in the sea urchin embryo.
2007,
Pubmed
,
Echinobase
Wu,
Twist is an essential regulator of the skeletogenic gene regulatory network in the sea urchin embryo.
2008,
Pubmed
,
Echinobase
Zigler,
Egg energetics, fertilization kinetics, and population structure in echinoids with facultatively feeding larvae.
2008,
Pubmed
,
Echinobase
