Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin embryo.
Abstract
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.
Type
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https://hdl.handle.net/10161/23878Published Version (Please cite this version)
10.1242/dev.198614Publication Info
Massri, Abdull J; Greenstreet, Laura; Afanassiev, Anton; Berrio, Alejandro; Wray,
Gregory A; Schiebinger, Geoffrey; & McClay, David R (2021). Developmental single-cell transcriptomics in the Lytechinus variegatus sea urchin
embryo. Development (Cambridge, England). 10.1242/dev.198614. Retrieved from https://hdl.handle.net/10161/23878.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
David R. McClay Jr.
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 bound
Gregory Allan Wray
Professor of Biology
I study the evolution of genes and genomes with the broad aim of understanding the
origins of biological diversity. My approach focuses on changes in the expression
of genes using both empirical and computational approaches and spans scales of biological
organization from single nucleotides through gene networks to entire genomes. At
the finer end of this spectrum of scale, I am focusing on understanding the functional
consequences and fitness components of specific genetic variants within reg
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