Single-cell analysis reveals prominent classes within the planarian stem cell compartment
Ontology highlight
ABSTRACT:
ORGANISM(S): Schmidtea mediterranea
PROVIDER: GSE58057 | GEO | 2014/09/30
REPOSITORIES: GEO
Similar Datasets
Project description:Single cell qPCR analysis identified two prominent expression signatures within the planarian stem cells, the neoblasts. RNAi against zinc finger protein zfp-1 results in elimination of one of the two classes. Worms were treated with RNAi by feeding. X1 or X2 cells were isolated by FACS, or blastemas were dissected. mRNA libraries were sequenced.
2014-09-30 | E-GEOD-58057 | biostudies-arrayexpress
Project description: Not available
| S-EPMC4171737 | biostudies-literature
Project description:Freshwater planarian flatworms possess uncanny regenerative capacities mediated by abundant and collectively totipotent adult stem cells. Key functions of these cells during regeneration and tissue homeostasis have been shown to depend on PIWI, a molecule required for piRNA expression in planarians. Nevertheless, the full complement of piRNAs, and microRNAs (miRNAs) in this organism has yet to be defined. Here, we report on the large scale cloning and sequencing of small RNAs from the planarian Schmidtea mediterranea, yielding altogether millions of sequenced unique small RNAs. We show that piRNAs are in part organized in genomic clusters and that they share characteristic features with mammalian and fly piRNAs. We further identify 61 novel miRNA genes and thus double the number of known planarian miRNAs. Sequencing, as well as quantitative PCR of small RNAs uncovered ten miRNAs enriched in planarian stem cells. These miRNAs are down-regulated in animals in which stem cells have been abrogated by irradiation, and thus constitute miRNAs likely associated with specific stem cell functions. Altogether, we present the first comprehensive small RNA analysis in animals belonging to the third animal superphylum, the Lophotrochozoa, and single out a number of miRNAs that may function in regeneration. Several of these miRNAs are deeply conserved in animals. Small RNAs were sequenced from FACS-sorted neoblast stem cells, untreated planarians and irradiated planarians, depleted of neoblasts
2009-06-30 | E-GEOD-16159 | biostudies-arrayexpress
Project description:Regeneration is the regrowth of damaged tissues or organs, a vital mechanism in response to damages from primitive organisms to higher mammals. Planarian possesses active whole-body regenerative capability owning to its vast reservoir of adult stem cells, neoblasts, providing an ideal model to delineate the underlying mechanisms for regeneration. RNA N6-methyladenosine (m6A) modification participates in many biological processes, including stem cell self-renewal and differentiation, in particular the regeneration of hematopoietic stem cells and axons. However, how m6A controls regeneration at the whole-organism level remains largely unknown. Here, we demonstrate that the depletion of m6A methyltransferase regulatory subunit wtap abolishes planarian regeneration, potentially through regulating genes related to cell-cell communication and cell cycle. Single-cell RNA-seq (scRNA-seq) analysis unveils that the wtap knockdown induces a unique type of neural progenitor-like cells (NP-like cells), characterized by specific expression of the cell-cell communication ligand grn. Intriguingly, the depletion of m6A-modified transcripts grn/cdk9 (or cdk7) axis rescues the defective regeneration of planarian caused by wtap knockdown. Overall, our study reveals an indispensable role of m6A modification in regulating whole-organism regeneration.
2023-04-28 | GSE202928 | GEO
Project description:The transcriptome of the planarian Schmidtea mediterranea is not well characterized. We have used RNA-Seq to characterize the transcriptome in both sexual and asexual strains of S. mediterranea from both untreated and irradiated animals. Moreover, we have performed RNA-Seq on RNA purified from FACS sorted neoblasts and differentiated cells. Together these studies expand our understanding of the planarian transcriptome and have identified strain-specific, neoblast-specific, and conserved transcripts. RNA-Seq was performed on RNA isolated from untreated and irradiated S. mediterranea animals from both the sexual and asexual strains, on FACS purified X1 neoblasts, X2 neoblasts, and Xins differentiated cells. One of the raw data files for GSM847465 is missing. The fasta file is provided at http://genome.vcell.uchc.edu/GenomeData02/Graveley_Lab_Public_Data/Planarian/S.mediterranea_SexNIRmRNA3.fa.gz
2012-04-24 | E-GEOD-34326 | biostudies-arrayexpress
Project description:Adult stem cells are tissue-specific cells with the capacity to self-renew and differentiate to continually replace cells lost to normal physiological turnover or injury. Neoblasts, the planarian stem cells, are widely distributed throughout the body mesenchyme, driving constitutive renewal of tissues during homeostasis and endowing planarians with the remarkable capacity to regenerate wholly from tiny tissue fragments. Neoblasts are the only dividing cells in planarians and are believed to be collectively comprised of both a heterogeneous population of pluripotent cells with broad differentiation potential and also lineage-committed progenitor cells that give rise to specific tissues. Recent work has identified a prominent class of neoblasts referred to as zeta-class, which express the zinc-finger gene zfp-1. Zfp-1, along with the chromatin remodeling factor chd4, the tumor suppressor gene p53, and most recently an RNA-binding protein mex3-1, have all been shown to be required for maintenance of two related post-mitotic, sub-epidermal cell populations expressing the specific marker genes prog-1 and AGAT-1, which have been widely used to asses neoblast differentiation. Given that zeta-class neoblasts are required for the generation of prog-1 and AGAT-1 positive cells and other markers of epidermal cell types, prog-1 and AGAT-1 likely mark two major populations of epidermal progeny cells. To understand the molecular mechanisms underlying neoblast differentiation and how they give rise to multiple cell types, we devised a strategy to identify critical factors enriched in the AGAT-1 positive cell population required for epidermal lineage progression. We performed RNA-Seq analysis of chd4 and p53 RNAi animals and characterized additional markers enriched in AGAT-1 positive and related post-mitotic cells.
2015-10-21 | GSE72389 | GEO
Project description:We have developed an accurate and reliable mass-spectra-based proteomics approach to complement previous genomic studies and to further achieve a more accurate understanding and description of the molecular and cellular processes related to the neoblasts.
2012-03-05 | PRD000350 | Pride
Project description:Difficulty of experimental accessing makes in vivo stem cell studies not easy in mammals and model systems with regenerative capability represent an alternative for the characterization of stem cell-specific genes. Planarians retain a population of pluripotent stem cells, the neoblasts, throughout their adult life. Neoblasts can be selectively destroyed by X-ray allowing us to compare stem cell-less organisms with wild-type worms. We have undertaken a genomic approach producing an Keywords: X-ray, dose response, stem cells, stress response
2006-07-19 | GSE5318 | GEO
Project description:Neoblasts are adult stem cells (ASCs) in planarians which sustain cell replacement during homeostasis and regeneration of any missing tissue. While numerous studies have examined genes underlying neoblast pluripotency, molecular pathways driving the postmitotic fate remain poorly defined. Here we used transcriptional profiling of irradiation-sensitive and -insensitive cell populations and RNA interference (RNAi) functional screening to uncover markers and regulators of postmitotic progeny. We identified 32 new markers, which distinguish two epithelial progenitor populations, and a planarian homolog to the MEX3 RNA-binding protein (Smed-mex3-1) as a key regulator of lineage progression. mex3-1 is required for generating progenitors of epithelial, neural, eye, pharyngeal, and protonephridial lineages, and restricting expansion of the stem cell compartment. We also demonstrate the utility of using mex3-1(RNAi) animals to identify additional progenitor markers. These results show that mex3-1 promotes differentiation in multiple, if not all, lineages, and maintains the balance between ASC self-renewal and commitment. Sorted and irradiated animals were collected as previously described (Labbe, et al., 2012) and RNAi conditions were triplicated, RNA was purified independently, then each replicate was pooled in equal amounts for sequencing at the timepoint: 1 feed day 12 for control RNAi and mex3-1 RNAi.
2015-06-15 | E-GEOD-68581 | biostudies-arrayexpress
Project description:Neoblasts are adult stem cells (ASCs) in planarians which sustain cell replacement during homeostasis and regeneration of any missing tissue. While numerous studies have examined genes underlying neoblast pluripotency, molecular pathways driving the postmitotic fate remain poorly defined. Here we used transcriptional profiling of irradiation-sensitive and -insensitive cell populations and RNA interference (RNAi) functional screening to uncover markers and regulators of postmitotic progeny. We identified 32 new markers, which distinguish two epithelial progenitor populations, and a planarian homolog to the MEX3 RNA-binding protein (Smed-mex3-1) as a key regulator of lineage progression. mex3-1 is required for generating progenitors of epithelial, neural, eye, pharyngeal, and protonephridial lineages, and restricting expansion of the stem cell compartment. We also demonstrate the utility of using mex3-1(RNAi) animals to identify additional progenitor markers. These results show that mex3-1 promotes differentiation in multiple, if not all, lineages, and maintains the balance between ASC self-renewal and commitment.
2015-06-15 | GSE68581 | GEO