Supplemental Materials for Ta., et al 2021

Amphibian metamorphosis is a transitional period that involves significant changes in the cell type populations and biological processes occurring in the brain. Analysis of gene expression dynamics during this process may provide insight into the molecular events underlying these changes. We conducted differential gene expression analyses of the developing X. laevis tadpole brain during this period in two ways: first, over stages of development in the midbrain, and second, across regions of the brain at a single developmental stage. We found that genes pertaining to positive regulation of neural progenitor cell proliferation as well as known progenitor cell markers were upregulated in the midbrain prior to metamorphic climax; concurrently, expression of cell cycle timing regulators decreased across this period, supporting the notion that cell cycle lengthening contributes to a decrease in proliferation by the end of metamorphosis. We also found that at the start of metamorphosis, neural progenitor populations appeared to be similar across the fore-, mid-, and hindbrain regions. Genes pertaining to negative regulation of differentiation were upregulated in the spinal cord compared to the rest of the brain, however, suggesting that a different program may regulate neurogenesis there. Finally, we found that regulation of biological processes like cell fate commitment and synaptic signaling follow similar trajectories in the brain across early tadpole metamorphosis and mid- to late-embryonic mouse development. By comparing expression across both temporal and spatial conditions, we have been able to illuminate cell type and biological pathway dynamics in the brain during metamorphosis.

All raw X. laevis data and processed counts are available on in the GEO repository as [GSE183193]. All data are available as supplemental files on the GSA FigShare portal. The aligned read statistics are provided in the supplemental material as Supplementary Data S1. The table constructed for conversion of gene symbols from X. laevis to H. sapiens is provided as Supplementary Data S2. The full differential expression analysis results for the by-stage comparison in the midbrain is provided as S3; for the by-region comparison at stage 46 as S7. Full GO term analyses results for these comparisons are provided as S5 for the by-stage comparison and S8 for the by-region comparison. The list of cell type markers used to test for enrichment in the by-stage comparison are given as S4; the genes annotated as positively regulating proliferation in the same comparison are listed in S6. The differential expression analysis in mouse comparing the cortex and cerebellum, and the analysis comparing stages within each region, are provided as S9 and S10, respectively. The full GO term analysis comparing these genes in X. laevis is given in S11.