Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis

Abstract

A hallmark of animal evolution is the emergence and diversification of cell type-specific transcriptional states. But systematic and unbiased characterization of differentiated gene regulatory programs was so far limited to specific tissues in a few model species. Here, we perform whole-organism single cell transcriptomics to map cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal that display complex tissue-level bodyplan organization. We uncover high diversity of transcriptional states in Nematostella, demonstrating cell type-specific expression for 35% of the genes and 51% of the transcription factors (TFs) detected. We identify eight broad cell clusters corresponding to cell classes such as neurons, muscles, cnidocytes, or digestive cells. These clusters comprise multiple cell modules expressing diverse and specific markers, uncovering in particular a rich repertoire of cells associated with neuronal markers. TF expression and sequence analysis defines the combinatorial code that underlies this cell-specific expression. It also reveals the existence of a complex regulatory lexicon of TF binding motifs encoded at both enhancer and promoters of Nematostella tissue-specific genes. Whole organism single cell RNA-seq is thereby established as a tool for comprehensive study of genome regulation and cell type evolution.Non-bilaterian animal lineages, including cnidarians, ctenophores, sponges and placozoans, have simple body plans and have been historically considered to contain limited numbers of cell types (Valentine, 2003). In cnidarians, these cells include a small number of morphologically distinct neurons, gland cells, muscle cells, epidermis, and gut (Frank and Bleakney, 1976;Hand and Uhlinger, 1992;Hyman, 1940). This presumed simplicity in the number of cnidarian cell types stands in marked contrast to their genomic complexity. Indeed, multiple genomic features, such as the gene repertoire, syntenic gene blocks, and intronic structure, are more similar between cnidarians and vertebrates than to model bilaterian invertebrates like D. melanogaster or C. elegans (Putnam et al., 2007;Technau and Schwaiger, 2015). Recently, it was shown that these similarities extend to the regulatory landscape of Nematostella genes (Schwaiger et al., 2014). However, the extent to which these genomic features participate in regulating complex cell type hierarchies remains largely unknown.Gene expression profiling by in situ hybridization allows for comparative study of cell types and tissue organisation in different species, providing insights into their evolution (Steinmetz et al., 2012). But these approaches require a priori selection of candidate gene markers; they are difficult to scale towards multiple expressed genes simultaneously; and they are not readily applicable to all species or life stages, in particular adult specimens. On the other hand, techniques for genome-wide profiling of gene expression were so far dependent on established staging and tissue dissection procedures. Single-cell RNA ...

Early metazoan cell type diversity and the evolution of multicellular gene regulation

“…However, comparative analysis of genomic regulatory programs in non-model organisms is confounded by the scarcity of direct molecular data on cell states and genome regulation. Whole-organism single cell RNAseq20,21 opens an opportunity to start closing this gap, by performing extensive sampling of transcriptional programs and characterizing cell type repertoires in diverse metazoan lineages. Here, we generate transcriptional maps at single cell resolution for A.queenslandica , M.leidyi and T.adhaerens .…”

Signaling via GABAB receptors regulates early development and neurogenesis in the basal metazoan Nematostella vectensis

“…Another homolog, v1g243252, had eight predicted TM helices (predicted by three different prediction servers, see Materials and Methods) and a ~300 residue domain of unknown function (DUF4475) located after these TM domains. 6 To test if the identified GABABR homologs exhibit neuronal-related expression, we searched the recently published Nematostella cell type expression atlas (43), quantifying the expression of the eight GABABR homologs ( Supplementary Fig. 4).…”