Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts acrossClytiamedusa cell types

Abstract

We present an organism-wide, transcriptomic cell atlas of the hydrozoan medusa Clytia hemisphaerica and describe how its component cell types respond to perturbation. Using multiplexed single-cell RNA sequencing, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run, we avoid artifacts from batch effects and are able to discern shifts in cell state in response to organismal perturbations. This work serves as a foundation for future studies of development, function, and regeneration in a genetically tractable jellyfish species. Moreover, we introduce a powerful workflow for high-resolution, whole-animal, multiplexed single-cell genomics that is readily adaptable to other traditional or nontraditional model organisms.

A novel regulatory gene promotes novel cell fate by suppressing ancestral fate in the sea anemoneNematostella vectensis

“…Thus, we present a complete cnidocyte character identity network which includes the genes necessary for activation of new character traits and suppression of ancestral traits ( 48 ), and provide a mechanistic explanation for the development of a truly novel cell type. Given the similar expression of ZNF845 in hydrozoans, in the progenitor cell population that gives rise to cnidocytes ( 17 ), we suggest the results presented here may reflect a broader phenomenon—that this cnidarian-specific gene ( ZNF845 ) was essential for the emergence of a cnidarian-specific cell type (cnidocytes) in the ancestor of all cnidarians.…”

“…Paired with the coexpression results, these data suggest that ZNF845 is part of the cnidogenesis pathway acting upstream of PaxA . In support of this hypothesis, a recent study using single-cell RNA sequencing (RNA-seq) in the hydrozoan Clytia hemisphaerica revealed ZNF845 was expressed specifically in the subpopulation of interstitial stem cells that goes on to become cnidocytes ( 17 ). Together, these results suggest that ZNF845 plays a similar role in the early patterning of cnidocytes in two distantly related cnidarians and may not be a general marker of stem cell fate, as once thought.…”

“…Here, we show explicitly that no bilaterian ZNF gene is the reciprocal best BLAST hit for cnidarian ZNF845 (NCBI accession for N. vectensis : XP_001641179.2). As such, we suggest changing the name of the cnidarian gene formerly called ZNF845 ( 15 , 17 , 33 – 36 ) to CnZNF1 . Renaming the gene this way accomplishes two things: first, the prefix “Cn” denotes that this is a cnidarian-specific transcription factor; second, this naming scheme reduces any confusion that derives from the fact that the name ZNF845 is already associated with a human gene that has a distinct evolutionary history.…”

Neural Cell Type Diversity in Cnidaria

“…In Nematostella vectensis a transgenic Elav-mOrange reporter is widely expressed in the nervous system, but the line appears to not express pan-neuronally since other neuronal reporter lines are not completely overlapping with the Elav-mOrange reporter ( Nakanishi et al, 2012 ). Single-cell transcriptomics also identified Elav as neuronal marker in Clytia ( Chari et al, 2021 ). The pan-neuronal Hydra Gcamp line described above made use of an actin -promotor, a gene family that is not exclusively expressed in the nervous system, but cytoskeletal genes are often strongly enriched in the nervous system and some genes may contain nervous system specific enhancers ( Dupre and Yuste, 2017 ).…”

siRNA-mediated gene knockdown via electroporation in hydrozoan jellyfish embryos

“…Indeed, gene silencing by morpholino oligos and mRNA microinjection as well as gene knockout via CRISPR/Cas9 allow for the investigation of the functions of genes of interest [9][10][11][12][13] . Furthermore, the Clytia genome assembly is complete, and transcriptome profiles are available for various stages and tissues, even at the single-cell level, which creates the foundation for research at the molecular level 12,[14][15][16][17][18] . These resources and techniques, together with recently-established transgenesis 19 , accelerate research into different features associated with distinct Clytia life stages.…”