Regulation of dynamic pigment cell states at single-cell resolution

Abstract

Cells bearing pigment have diverse roles and are often under strict evolutionary selection. Here, we explore the regulation of pigmented cells in the purple sea urchin Strongylocentrotus purpuratus, an emerging model for diverse pigment function. We took advantage of single cell RNA-seq (scRNAseq) technology and discovered that pigment cells in the embryo segregated into two distinct populations, a mitotic cluster and a post-mitotic cluster. Gcm is essential for expression of several genes important for pigment function, but is only transiently expressed in these cells. We discovered unique genes expressed by pigment cells and test their expression with double fluorescence in situ hybridization. These genes include new members of the fmo family that are expressed selectively in pigment cells of the embryonic and in the coelomic cells of the adult - both cell-types having immune functions. Overall, this study identifies nodes of molecular intersection ripe for change by selective evolutionary pressures.

Single cell RNA sequencing of theStrongylocentrotus purpuratuslarva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome

“…Overall, this cluster exhibited greatest transcriptional similarity to cell types derived from the ectoderm (Figure 1- Figure supplement 1E), suggesting it may be of ectodermal origin. Consistent with this, a recent study revealed a similar uncharacterized ectodermal cell type (Perillo et al, 2020), further suggesting this cell population exists and is not solely an artifact of our analysis. Taking into account the great plasticity and regeneration capability of the sea urchin larva, it is also possible that this non-differentiated ectodermal cell type is a progenitor population in stasis, waiting to be activated.…”

Developmental Single-cell transcriptomics in theLytechinus variegatusSea Urchin Embryo

“…To map known GRN genes, and to identify novel candidates during this critical time period of embryonic development, we performed a scRNA-seq analysis using the 10x Genomics system. This standardized and reproducible advanced scRNA-seq platform yields relatively deep coverage of RNA expression in single cells at a cost that is not prohibitive (Massri et al, 2021; Perillo et al, 2020). Eighteen timepoints were collected, initially at hourly intervals and then during later stages at two to four hour intervals.…”

“…Many perturbations of transcription factors and signals from multiple laboratories revealed a detailed network model that operates from fertilization until gastrulation (Davidson et al, 2002; McClay et al, 2020; Peter and Davidson, 2015). Recently, scRNA-seq was used to compile the first atlas of development for Strongylocentrotus purpuratus ( Sp ) (Foster et al, 2020), and that approach was further used to explore the development of pigment cells in Sp (Perillo et al, 2020). Given the extensive knowledge of dGRNs in the sea urchin embryo, and taking advantage of the methods for scRNA-seq developed for this model embryo {Massri, 2021; Perillo et al, 2020), our first goal was to establish whether the molecules in dGRNs were “visible” to scRNA-seq inquiries.…”

“…Recently, scRNA-seq was used to compile the first atlas of development for Strongylocentrotus purpuratus ( Sp ) (Foster et al, 2020), and that approach was further used to explore the development of pigment cells in Sp (Perillo et al, 2020). Given the extensive knowledge of dGRNs in the sea urchin embryo, and taking advantage of the methods for scRNA-seq developed for this model embryo {Massri, 2021; Perillo et al, 2020), our first goal was to establish whether the molecules in dGRNs were “visible” to scRNA-seq inquiries. We find that more than 98% of the molecules in the sea urchin dGRN are present in our scRNA-seq database, both in the lineages expected and at the times the dGRN models indicate those signals and transcription factors are present to guide specification.…”

Functional contribution of DCLKs in sea urchin development

“…The signal was uniformly distributed during early embryogenesis yet became enriched in mesenchymal cells after the gastrula stage as well as in skeletal rods (Figure 2C, arrows). Not all but some of these DCLK positive cells were also detected by SP1, a pigment cell marker (Figure 2D, arrows) 13,14 . Further, some of the RB1 positive cells were also detected by SP1(Figure 2D, arrows).…”