Using Single Cell Omics to Understand Posterior Neural Crest Differentiation in Zebrafish

Abstract

Neural crest cells (NCCs) are a migratory, multipotent, and transient stem cell population essential to vertebrate development. Born along the neural tube, NCCs are regionally specified along the anterior‐posterior axis to contribute to a vast number of cell lineages; such as craniofacial cartilage, pigment cells, and large aspects of the peripheral nervous system. In our recently published single‐cell RNA‐sequencing (scRNA‐seq) analysis of posterior NCC lineages in zebrafish embryos, we discovered a combinatorial expression code of transcripts that encode for posterior Hox transcription factors, which was especially specific to NCC‐derived neural lineages. While Hox expression combinations had been characterized within pre‐migratory and recently delaminated cranial NCCs in prior studies, such a high‐resolution signature had not been described within the context of posterior NCC lineages during their differentiation. Here, we report a lifetime atlas of NCC and NCC‐derived cells along the posterior zebrafish body, greatly expanding our prior analyses. To achieve this, several published and publicly‐available zebrafish scRNA‐seq studies characterizing NCC and NCC‐derived cells were computationally merged with our prior data sets and integrated, encompassing: 24 hours post fertilization (hpf), 48‐50 hpf, 68‐70 hpf, 5 days post fertilization (dpf), juvenile, and adult tissues—producing a cohesive distribution of cell identities. Within the lifetime atlas, various Hox gene transcript signatures were observed where numerous discrete cell lineages formed over time and unique Hox expression codes resolved within these incipient lineages. The generation of a multi‐stage comprehensive transcriptional atlas from multiple scRNA‐seq studies will serve as a valuable tool for the NCC and zebrafish communities. Additionally, this atlas of cell lineages demonstrates the complexity and robustness of combinatorial Hox expression codes in posterior NCC throughout development and suggests possible functional roles therein.