Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions

Abstract

Background During embryogenesis, the developmental potential of initially pluripotent cells becomes progressively restricted as they transit to lineage restricted states. The pluripotent cells of Xenopus blastula-stage embryos are an ideal system in which to study cell state transitions during developmental decision-making, as gene expression dynamics can be followed at high temporal resolution. Results Here we use transcriptomics to interrogate the process by which pluripotent cells transit to four different lineage-restricted states: neural progenitors, epidermis, endoderm and ventral mesoderm, providing quantitative insights into the dynamics of Waddington’s landscape. Our findings provide novel insights into why the neural progenitor state is the default lineage state for pluripotent cells and uncover novel components of lineage-specific gene regulation. These data reveal an unexpected overlap in the transcriptional responses to BMP4/7 and Activin signaling and provide mechanistic insight into how the timing of signaling inputs such as BMP are temporally controlled to ensure correct lineage decisions. Conclusions Together these analyses provide quantitative insights into the logic and dynamics of developmental decision making in early embryos. They also provide valuable lineage-specific time series data following the acquisition of specific lineage states during development.

Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis

“…After genome activation, a heightened imbalance in favor of the L homeolog emerges, as measured by activation patterns in four differentiated cell lineages ( Johnson et al, 2022 ; Figure 2D , Figure 2—figure supplement 1E–I ), that appears to indicate a shift toward more divergent homeolog regulation as development proceeds, as was observed previously ( Session et al, 2016 ). However, it is likely that some of the shared homeolog activation as measured in the whole blastula is actually composed of homeolog-specific regional activation ( Chen and Good, 2022 ).…”

“…Right, homeolog proportions of later gene activation in epidermal (Epi), neural progenitor (Neur), ventral mesodermal (Meso), and endodermal (Endo) lineages from stages 10–13 (p=3.3 × 10 –64 , χ-squared test comparing stage 9 and the four lineages, 16 d.o.f.). Lineage-specific gene expression data are from Johnson et al, 2022 . ( E ) Homeolog-specific stage 9 activation proportions, versus maternal contribution homeolog expression patterns, for maternal-zygotic genes.…”

“…Top plots represent all genes increased at each stage, bottom plots represent genes with maternal contribution <1 TPM. Lineage-specific gene expression data are from Johnson et al, 2022 . ( F ) Proportion of genes encoded on both subgenomes that change homeolog activation patterns in a differentiated lineage in stages 10–13.…”

SoxB1 transcription factors are essential for initiating and maintaining the neural plate border gene expression

“…We also examined changes in levels of Sox3 protein over time in three different ectodermal cell populations: neural plate border, epidermal, and neural cells via western blot. Untreated blastula stem cells become epidermis due to endogenous BMP signaling (Wilson et al, 1997) and a neural state can be induced using a high dosage of BMPi (Johnson et al, 2022). Explants for each ectodermal cell type were collected at time points corresponding with blastula stage (stage 9) through mid-neurula (stage 15) and endogenous levels of Sox3 were assessed via western blot and quantified, normalizing using actin (Fig.…”

Shared features of blastula and neural crest stem cells evolved at the base of vertebrates

“…Although pou5 and ventx / nanog are not encoded in invertebrate chordate genomes 9,65,66 , invertebrate chordates do express homologs of the neural stem cell factors soxB1 and myc in the blastula 17 . Thus the precursors of the vertebrate pluripotency GRN may have arisen in cells fated to be neural progenitor cells, perhaps explaining why the neural lineage has been found to lie closest in gene regulatory state space to pluripotent blastula cells and why several neural crest regulatory factors have been found to have deep roots in bilaterian neurogenesis 4,67,68 .…”