BirthSeq, a new method to isolate and analyze dated cells from any tissue in vertebrates

Abstract

Embryonic development is a complex and dynamic process that unfolds over time and involves the production of increasing numbers of cells, as well as the diversification of different cell types. The impact of developmental time on the formation of the central nervous system is well documented, with evidence showing that time plays a critical role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via FACS, and analysis using high-throughput techniques. We demonstrate the effectiveness of BirthSeq for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in brain development across three vertebrate species (mouse, chick, and gecko). Overall, BirthSeq provides a versatile tool for studying any tissue in any vertebrate organism, helping to fill the necessity in developmental biology research by targeting cells and their temporal cues.

Adeno-Associated Viral Tools to Trace Neural Development and Connectivity Across Amphibians

“…Our results indicate that, like in mammals, complex brain regions such as the pallium and the optic tectum are built by adding new neurons in precise temporal patterns (layers in the pallium or cortex, wedges in the optic tectum or superior colliculus, and dorso-ventral domains in the spinal cord) also in amphibians. AAVs, in combination with scRNAseq or spatial transcriptomics, will enable a comparison of the molecular identities and projections of neurons generated in the same relative order in different species 131 . Going beyond individual brain regions, labeling and manipulating isochronic cohorts of neurons in the entire CNS may be used to investigate the relationships between neuronal birthdate and connectivity, and to test, for example, the hypothesis that neurons that are born together wire together 127 .…”