Transcriptome Analysis Reveals Strain-Specific and Conserved Stemness Genes in Schmidtea mediterranea

Abstract

The planarian Schmidtea mediterranea is a powerful model organism for studying stem cell biology due to its extraordinary regenerative ability mediated by neoblasts, a population of adult somatic stem cells. Elucidation of the S. mediterranea transcriptome and the dynamics of transcript expression will increase our understanding of the gene regulatory programs that regulate stem cell function and differentiation. Here, we have used RNA-Seq to characterize the S. mediterranea transcriptome in sexual and asexual animals and in purified neoblast and differentiated cell populations. Our analysis identified many uncharacterized genes, transcripts, and alternatively spliced isoforms that are differentially expressed in a strain or cell type-specific manner. Transcriptome profiling of purified neoblasts and differentiated cells identified neoblast-enriched transcripts, many of which likely play important roles in regeneration and stem cell function. Strikingly, many of the neoblast-enriched genes are orthologs of genes whose expression is enriched in human embryonic stem cells, suggesting that a core set of genes that regulate stem cell function are conserved across metazoan species.

The ancestral gene repertoire of animal stem cells

“…2C and Dataset S2, Table S6). Some genes overexpressed in archeocytes and with orthologs having known stem-cell functions in other animals do not appear among the 180 genes, due, for instance, to secondary gene loss in H. vulgaris or S. mediterranea (e.g., Myc is missing in flatworm) (28) or because they are also highly expressed in the unipotent epithelial stem cells of H. vulgaris (e.g., Piwi) or differentiated cells of S. mediterranea (e.g., GATA1-4). Interestingly, although the foldchange thresholds initially used to select stem-cell genes in the three species were permissive (Methods), the resulting 180 genes rank among the most strongly overexpressed in stem cells (in Ephydatia the median ratio of expression in archeocytes for these 180 genes is 4.3-fold over other cells and 9.5-fold over choanocytes).…”

Genome-wide analysis of the bHLH gene family in planarians identifies factors required for adult neurogenesis and neuronal regeneration

“…S1, Table S1; for brevity we have omitted the Smed prefix from the gene names). Recent transcriptional profiles generated from sorted cell populations indicate that most bHLH homologs are expressed in the planarian stem cells and their postmitotic progeny (Labbé et al, 2012;Önal et al, 2012;Resch et al, 2012). To investigate cell-and tissue-specific patterns of bHLH gene expression, we performed whole mount in situ hybridization (WISH).…”

Specialized progenitors and regeneration

“…Furthermore, many genes are commonly expressed in cells that have these features (morphology, localization, division, irradiation sensitivity), and the expression of such genes has been used to label a cell as a neoblast (Shibata et al, 1999;Reddien et al, 2005b;Salvetti et al, 2005;Guo et al, 2006;Palakodeti et al, 2008;Solana et al, 2009;Fernandéz-Taboada et al, 2010;Rouhana et al, 2010;Shibata et al, 2010;Labbé et al, 2012;Onal et al, 2012;Resch et al, 2012;Shibata et al, 2012;Solana et al, 2012;Wagner et al, 2012). Many of the genes that are expressed broadly, if not uniformly, in the neoblast population encode proteins similar to those found in germ cells in other organisms, suggesting a germ cell-like character of cells throughout the neoblast population.…”

“…The capacity of fragments of planarians from any region containing neoblasts to regenerate suggests that the attribute of pluripotency (defined here as the capacity to generate somatic lineages spanning RNA probes for particular neoblast-expressed genes Labbé et al, 2012;Onal et al, 2012;Resch et al, 2012;Shibata et al, 2012;Solana et al, 2012;Wagner et al, 2012 *This table is not intended to present a comprehensive list of key gene expression attributes of neoblasts nor all methods historically used to visualize neoblasts. ‡ Additional morphological attributes, such as blebs and projections, have been described for the cNeoblast (Wagner et al, 2011).…”