scholarly journals Deployment of a retinal determination gene network drives directed cell migration in the sea urchin embryo

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Megan L Martik ◽  
David R McClay
Keyword(s):  
Sea Urchin ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Regulatory Control ◽  
Directed Cell Migration ◽  
Multipotent Progenitors ◽  
Retinal Determination ◽  
Sea Urchin Embryo ◽  
Gene Regulatory ◽  
Retinal Determination Gene Network

Gene regulatory networks (GRNs) provide a systems-level orchestration of an organism's genome encoded anatomy. As biological networks are revealed, they continue to answer many questions including knowledge of how GRNs control morphogenetic movements and how GRNs evolve. The migration of the small micromeres to the coelomic pouches in the sea urchin embryo provides an exceptional model for understanding the genomic regulatory control of morphogenesis. An assay using the robust homing potential of these cells reveals a ‘coherent feed-forward’ transcriptional subcircuit composed of Pax6, Six3, Six1/2, Eya, and Dach1 that is responsible for the directed homing mechanism of these multipotent progenitors. The linkages of that circuit are strikingly similar to a circuit involved in retinal specification in Drosophila suggesting that systems-level tasks can be highly conserved even though the tasks drive unrelated processes in different animals.

scholarly journals Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo

Development ◽  
2021 ◽  
Author(s):  
Abdull J. Massri ◽  
Laura Greenstreet ◽  
Anton Afanassiev ◽  
Alejandro Berrio ◽  
Gregory A. Wray ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Regulatory Networks ◽  
Developmental Trajectories ◽  
Primordial Germ Cell ◽  
Equatorial Region ◽  
Lytechinus Variegatus ◽  
Sea Urchin Embryo ◽  
Transcriptional Changes ◽  
Gene Regulatory ◽  
Cell Trajectories

Using scRNA-seq coupled with computational approaches, we studied transcriptional changes in cell states of sea urchin embryos during development to the larval stage. Eighteen closely spaced time points were taken during the first 24 hours of development of Lytechinus variegatus (Lv). Developmental trajectories were constructed using Waddington-OT, a computational approach to "stitch" together developmental timepoints. Skeletogenic and primordial germ cell trajectories diverged early in cleavage. Ectodermal progenitors were distinct from other lineages by sixth cleavage, though a small percentage of ectoderm cells briefly co-expressed endoderm markers indicating an early ecto-endoderm cell state, likely in cells originating from the equatorial region of the egg. Endomesoderm cells originated at 6th cleavage also and this state persisted for more than two cleavages, then diverged into distinct endoderm and mesoderm fates asynchronously, with some cells retaining an intermediate specification status until gastrulation. 79 of 80 genes (99%) examined, and included in published developmental gene regulatory networks (dGRNs), are present in the Lv-scRNA-seq dataset, and expressed in the correct lineages in which the dGRN circuits operate.

scholarly journals Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks

2003 ◽  
Vol 261 (1) ◽  
pp. 55-81 ◽  
Author(s):  
Gabriele Amore ◽  
Robert G Yavrouian ◽  
Kevin J Peterson ◽  
Andrew Ransick ◽  
David R McClay ◽  
...  
Keyword(s):  
Sea Urchin ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Sea Urchin Embryo ◽  
Oral Ectoderm ◽  
Gene Regulatory

scholarly journals The tolerance to hypoxia is defined by a time-sensitive response of the gene regulatory network in sea urchin embryos

Development ◽  
2021 ◽  
pp. dev.195859
Author(s):  
Majed Layous ◽  
Lama Khalaily ◽  
Tsvia Gildor ◽  
Smadar Ben-Tabou de-Leon
Keyword(s):  
Early Development ◽  
Sea Urchin ◽  
Regulatory Networks ◽  
Normal Development ◽  
Axis Formation ◽  
Oxygen Level ◽  
Sea Urchin Embryo ◽  
Tolerance To Hypoxia ◽  
Vegf Pathway ◽  
Gene Regulatory

Deoxygenation, the reduction of oxygen level in the oceans induced by global warming and anthropogenic disturbances, is a major threat to marine life. This change in oxygen level could be especially harmful to marine embryos that utilize endogenous hypoxia and redox gradients as morphogens during normal development. Here we show that the tolerance to hypoxic conditions changes between different developmental stages of the sea urchin embryo, possibly due to the structure of the gene regulatory networks (GRNs). We demonstrate that during normal development, bone morphogenetic protein (BMP) pathway restricts the activity of the vascular endothelial growth factor (VEGF) pathway to two lateral domains and by that controls proper skeletal patterning. Hypoxia applied during early development strongly perturbs the activity of Nodal and BMP pathways that affect VEGF pathway, dorsal-ventral (DV) and skeletogenic patterning. These pathways are largely unaffected by hypoxia applied after DV-axis formation. We propose that the use of redox and hypoxia as morphogens makes the sea urchin embryo highly sensitive to environmental hypoxia during early development, but the GRN structure provides higher tolerance to hypoxia at later stages.

scholarly journals BioNetLink - An Architecture for Working with Network Data

2014 ◽  
Vol 11 (2) ◽  
pp. 68-79
Author(s):  
Matthias Klapperstück ◽  
Falk Schreiber
Keyword(s):  
Experimental Data ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Large Data ◽  
Biological Data ◽  
Network Data ◽  
Data Sets ◽  
Dynamic Views ◽  
Gene Regulatory ◽  
Multiple Network

Summary The visualization of biological data gained increasing importance in the last years. There is a large number of methods and software tools available that visualize biological data including the combination of measured experimental data and biological networks. With growing size of networks their handling and exploration becomes a challenging task for the user. In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction networks. Therefore, fast access, abstract and dynamic views, and intuitive exploratory methods should be provided to search and extract information from the networks. This paper will introduce a conceptual framework for handling and combining multiple network sources that enables abstract viewing and exploration of large data sets including additional experimental data. It will introduce a three-tier structure that links network data to multiple network views, discuss a proof of concept implementation, and shows a specific visualization method for combining metabolic and gene regulatory networks in an example.

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