Journal Article

Cell type transcriptome atlas for the planarian Schmidtea mediterranea

Wurtzel, Omri, Kravarik, Kellie M., Reddien, Peter W., Fincher, Christopher T., de Hoog, Thom

2018

Overview

A cell type's transcriptome defines the active genes that control its biology. Two groups used single-cell RNA sequencing to define the transcriptomes for essentially all cell types of a complete animal, the regenerative planarian Schmidtea mediterranea. Because pluripotent stem cells constantly differentiate to rejuvenate any part of the body of this species, all developmental lineages are active in adult animals. Fincher et al. determined the transcriptomes for most, if not all, planarian cell types, including some that were previously unknown. They also identified transition states and genes governing positional information. Plass et al. used single-cell transcriptomics and computational algorithms to reconstruct a lineage tree capturing the developmental progressions from stem to differentiated cells. They could then predict gene programs that are specifically turned on and off along the tree, and they used this approach to study how the cell types behaved during regeneration. These whole-animal transcriptome “atlases” are a powerful way to study metazoan biology. Science , this issue p. eaaq1736 , p. eaaq1723 Single-cell RNA sequencing identifies the transcriptomes for most to all cell types of a flatworm. The transcriptome of a cell dictates its unique cell type biology. We used single-cell RNA sequencing to determine the transcriptomes for essentially every cell type of a complete animal: the regenerative planarian Schmidtea mediterranea. Planarians contain a diverse array of cell types, possess lineage progenitors for differentiated cells (including pluripotent stem cells), and constitutively express positional information, making them ideal for this undertaking. We generated data for 66,783 cells, defining transcriptomes for known and many previously unknown planarian cell types and for putative transition states between stem and differentiated cells. We also uncovered regionally expressed genes in muscle, which harbors positional information. Identifying the transcriptomes for potentially all cell types for many organisms should be readily attainable and represents a powerful approach to metazoan biology.

• Publisher: The American Association for the Advancement of Science
• Subject: Active control / Adults / Algorithms / Animals / Atlases as Topic / Biological evolution / Biological research / Biology / Cell Lineage - genetics / Cell number / Cells - classification / Cells - cytology / Cells - metabolism / Clustering / Complexity / Computer applications / Embryos / Gene expression / Gene Expression Profiling - methods / Gene mapping / Gene sequencing / Genes / Genomes / Muscles / Nucleotide sequence / Organisms / Pattern formation / Planarians - cytology / Pluripotency / Precursors / Progressions / Regeneration / Ribonucleic acid / RNA / Schmidtea mediterranea / Sequence Analysis, RNA - methods / Single-Cell Analysis - methods / Stem cell transplantation / Stem cells / Stem Cells - metabolism / Tissue analysis / Tissues / Transcription factors / Transcriptome / Turbellaria / Uniqueness