Developmental Single-cell transcriptomics in the Lytechinus variegatus Sea Urchin Embryo


<jats:title>Abstract</jats:title><jats:p>Here we employed scRNA-seq coupled with computational approaches to examine molecular changes in cells during specification and differentiation. We examined the first 24 hours of development of the sea urchin <jats:italic>Lytechinus variegatus</jats:italic> (<jats:italic>Lv</jats:italic>) with 18 time points during which the embryo develops to the larval stage. Using Waddington-OT, the time points were computationally “stitched” together to calculate developmental trajectories. Skeletogenic cells displayed the expected immediate early divergence while other lineages diverged asynchronously, with many cells retaining an intermediate specification status until late in gastrulation. The <jats:italic>Lv</jats:italic>-scRNA-seq dataset was compared to the developmental Gene Regulatory Network (dGRN) model of specification in <jats:italic>Strongylocentrotus purpuratus</jats:italic> (<jats:italic>Sp</jats:italic>). 79 of 80 genes (98%) in that dGRN are present in the <jats:italic>Lv</jats:italic>-scRNA-seq dataset, and expressed in the correct lineages in which the dGRN circuits operate. Surprisingly, however, many heterochronies in timing of first expression of dGRN genes have evolved between the two species. Replotting the two dGRNs with precise attention to time of expression revealed a number of feedback inputs that likely buffer the dGRNs, allowing them to maintain function in the face of accumulating heterochronies.</jats:p><jats:sec><jats:title>Summary statement</jats:title><jats:p>The early development of the sea urchin embryo was followed using scRNA-seq plus computational methods to trace lineage diversifications. These were matched to gene regulatory network changes over time.</jats:p></jats:sec>






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Massri, Abdull, Laura Greenstreet, Anton Afanassiev, Alejandro Berrio Escobar, Gregory Wray, Geoffrey Schiebinger and David McClay (n.d.). Developmental Single-cell transcriptomics in the Lytechinus variegatus Sea Urchin Embryo. 10.1101/2020.11.12.380675 Retrieved from

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David R. McClay

Arthur S. Pearse Distinguished Professor of Biology

We ask how the embryo works. Prior to morphogenesis the embryo specifies each cell through transcriptional regulation and signaling. Our research builds gene regulatory networks to understand how that early specification works. We then ask how this specification programs cells for their morphogenetic movements at gastrulation, and how the cells deploy patterning information.
Current projects examine 1) novel signal transduction mechanisms that establish and maintain embryonic boundaries
mold the embryo at gastrulation; 2) specification of primary mesenchyme cells in such a way that they are prepared to execute an epithelial-mesenchymal transition, and then study mechanistically the regulation of that transition; 3) the specification of endoderm necessary for invagination of the archenteron; 4) formation of the oral/aboral ectoderm and the means by which patterning information is distributed three dimensionally around the embryo. That information is necessary for patterning and inducing skeletogenesis.
Other projects examine neural tube folding with the goal of identifying genes associated with neural tube defects. Finally, a large current effort in systems biology is being expended with the goal of enlarging our knowledge of early networks and how they interact.

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