Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding

A fundamental interest in developmental neuroscience lies in the ability to map the complete single-cell lineages within the brain. To this end, we developed a CRISPR editing-based lineage-specific tracing (CREST) method for clonal tracing in Cre mice. We then used two complementary strategies based on CREST to map single-cell lineages in developing mouse ventral midbrain (vMB). By applying snapshotting CREST (snapCREST), we constructed a spatiotemporal lineage landscape of developing vMB and identified six progenitor archetypes that could represent the principal clonal fates of individual vMB progenitors and three distinct clonal lineages in the floor plate that specified glutamatergic, dopaminergic or both neurons. We further created pandaCREST (progenitor and derivative associating CREST) to associate the transcriptomes of progenitor cells in vivo with their differentiation potentials. We identified multiple origins of dopaminergic neurons and demonstrated that a transcriptome-defined progenitor type comprises heterogeneous progenitors, each with distinct clonal fates and molecular signatures. Therefore, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification. CREST is a dual-recorder single-cell lineage tracing method for spatiotemporal mapping of the mouse brain.

Automated summary

A fundamental interest in developmental neuroscience is mapping single-cell lineages in the brain. Researchers developed a CRISPR editing-based lineage-specific tracing method called CREST and used it to map single-cell lineages in the developing mouse ventral midbrain (vMB). They identified different progenitor types and clonal lineages using the CREST method and associated progenitor cell transcriptomes with their differentiation potentials using pandaCREST. This comprehensive single-cell lineage analysis provides new insights into neural specification and offers a dual-recorder single-cell lineage tracing method for the mouse brain called CREST.