PT  - JOURNAL ARTICLE
AU  - Arnau Sebé-Pedrós
AU  - Elad Chomsky
AU  - Baptiste Saudememont
AU  - Marie-Pierre Mailhe
AU  - Flora Pleisser
AU  - Justine Renno
AU  - Yann Loe-Mie
AU  - Aviezer Lifshitz
AU  - Zohar Mukamel
AU  - Sandrine Schmutz
AU  - Sophie Nouvault
AU  - Francois Spitz
AU  - Amos Tanay
AU  - Heather Marlow
TI  - Cnidarian cell type diversity revealed by whole-organism single-cell RNA-seq analysis
AID  - 10.1101/201103
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 201103
4099  - http://biorxiv.org/content/early/2017/10/11/201103.short
4100  - http://biorxiv.org/content/early/2017/10/11/201103.full
AB  - 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.