Global irradiation effects, stem cell genes and rare transcripts in the planarian transcriptome

Abstract

Stem cells are the closest relatives of the totipotent primordial cell, which is able to spawn millions of daughter cells and hundreds of cell types in multicellular organisms. Stem cells are involved in tissue homeostasis and regeneration, and may play a major role in cancer development. Among animals, planarians host a model stem cell type, called the neoblast, which essentially confers immortality. Gaining insights into the global transcriptional landscape of these exceptional cells takes an unprecedented turn with the advent of Next Generation Sequencing methods. Two Digital Gene Expression transcriptomes of Schmidtea mediterranea planarians, with or without neoblasts lost through irradiation, were produced and analyzed. Twenty one bp NlaIII tags were mapped to transcripts in the Schmidtea and Dugesia taxids. Differential representation of tags in normal versus irradiated animals reflects differential gene expression. Canonical and non-canonical tags were included in the analysis, and comparative studies with human orthologs were conducted. Transcripts fell into 3 categories: invariant (including housekeeping genes), absent in irradiated animals (potential neoblast-specific genes, IRDOWN) and induced in irradiated animals (potential cellular stress response, IRUP). Different mRNA variants and gene family members were recovered. In the IRDOWN class, almost all of the neoblast-specific genes previously described were found. In irradiated animals, a larger number of genes were induced rather than lost. A significant fraction of IRUP genes behaved as if transcript versions of different lengths were produced. Several novel potential neoblast-specific genes have been identified that varied in relative abundance, including highly conserved as well as novel proteins without predicted orthologs. Evidence for a large body of antisense transcripts, for example regulated antisense for the Smed-piwil1 gene, and evidence for RNA shortening in irradiated animals is presented. Novel neoblast-specific candidates include a peroxiredoxin protein that appears to be preferentially expressed in human embryonic stem cells.

Transcriptional signatures of somatic neoblasts and germline cells in Macrostomum lignano

“…Both techniques proved to be efficient in determining the gene expression profile of planarian neoblasts (Reddien and Sánchez Alvarado, 2004; Hayashi et al, 2006; Rossi et al, 2007; Eisenhoffer et al, 2008; Blythe et al, 2010; Galloni, 2012; Shibata et al, 2012; Solana et al, 2012) and were, therefore, our first choice.…”

Single-Cell Analysis Reveals Functionally Distinct Classes within the Planarian Stem Cell Compartment

“…Furthermore, transcriptional analyses have identified many neoblast-enriched transcripts (Blythe et al, 2010; Eisenhoffer et al, 2008; Galloni, 2012; Labbe et al, 2012; Onal et al, 2012; Resch et al, 2012; Shibata et al, 2012; Solana et al, 2012; Wagner et al, 2012) including those encoding several Sox and Pou transcription factors, gene families with important roles in stem cell maintenance in other organisms. Neoblasts also express transcripts for the PIWI proteins Smedwi-1 and Smedwi-2 (Reddien et al, 2005b), the Bruno-like protein Bruli (Guo et al, 2006), and a Tudor protein (Solana et al, 2009).…”

The history and enduring contributions of planarians to the study of animal regeneration

“…In addition, the genome of the species Schmidtea mediterranea has been sequenced,74 to which EST, transcriptome, proteome, and small RNA datasets can be mapped 75–87. Genome microarrays have been generated to identify genes important for regeneration 59,88–91.…”