title: Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach.
abstract: BACKGROUND
  Planarian stem cells, or neoblasts, drive the almost unlimited regeneration capacities of freshwater planarians. Neoblasts are traditionally described by their morphological features and by the fact that they are the only proliferative cell type in asexual planarians. Therefore, they can be specifically eliminated by irradiation. Irradiation, however, is likely to induce transcriptome-wide changes in gene expression that are not associated with neoblast ablation. This has affected the accurate description of their specific transcriptomic profile.
  
  
  RESULTS
  We introduce the use of Smed-histone-2B RNA interference (RNAi) for genetic ablation of neoblast cells in Schmidtea mediterranea as an alternative to irradiation. We characterize the rapid, neoblast-specific phenotype induced by Smed-histone-2B RNAi, resulting in neoblast ablation. We compare and triangulate RNA-seq data after using both irradiation and Smed-histone-2B RNAi over a time course as means of neoblast ablation. Our analyses show that Smed-histone-2B RNAi eliminates neoblast gene expression with high specificity and discrimination from gene expression in other cellular compartments. We compile a high confidence list of genes downregulated by both irradiation and Smed-histone-2B RNAi and validate their expression in neoblast cells. Lastly, we analyze the overall expression profile of neoblast cells.
  
  
  CONCLUSIONS
  Our list of neoblast genes parallels their morphological features and is highly enriched for nuclear components, chromatin remodeling factors, RNA splicing factors, RNA granule components and the machinery of cell division. Our data reveal that the regulation of planarian stem cells relies on posttranscriptional regulatory mechanisms and suggest that planarians are an ideal model for this understudied aspect of stem cell biology.
authors.affiliation: Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, UK. Jordi.Solana@mdc-berlin.de
authors.forename: Jordi
authors.initials: J
authors.lastname: Solana
authors.forename: Damian
authors.initials: D
authors.lastname: Kao
authors.forename: Yuliana
authors.initials: Y
authors.lastname: Mihaylova
authors.forename: Farah
authors.initials: F
authors.lastname: Jaber-Hijazi
authors.forename: Sunir
authors.initials: S
authors.lastname: Malla
authors.forename: Ray
authors.initials: R
authors.lastname: Wilson
authors.forename: Aziz
authors.initials: A
authors.lastname: Aboobaker
mesh_terms: D000818:Animals; D002455:Cell Division / Q000235:genetics / Q000528:radiation effects; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism / Q000528:radiation effects; D005720:Gamma Rays; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000528:radiation effects; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D008522:Mediterranean Sea; D020411:Oligonucleotide Array Sequence Analysis; D010932:Planarians / Q000235:genetics* / Q000254:growth & development / Q000528:radiation effects; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism* / Q000528:radiation effects; D034622:RNA Interference; D012333:RNA, Messenger / Q000037:antagonists & inhibitors / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D006657:Histones; D012333:RNA, Messenger