ArticleNature methods2023
Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 26 citations in OpenAlex.
- Lineage-aware stochastic modeling reveals gene-expression dynamics in development and disease.bioRxiv : the preprint server for biology · 2026Article
- Lineage tracing from cellular heritage to disease destiny.Nature genetics · 2026Review
- Brain organoids and genome editing: A new era in understanding human brain development and disorders.Neural regeneration research · 2026Article
- Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data.Cell genomics · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings.PLoS computational biology · 2026Article
- A modeller's guide for biomedical discovery.Disease models & mechanisms · 2026Article
- AnnQ: reference-based quantification of cellular abnormality at single-cell resolution.Briefings in bioinformatics · 2026Article
- Distinct radial glia subtypes regulate midbrain dopaminergic neuron development.Nature neuroscience · 2026Article
- VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies.bioRxiv : the preprint server for biology · 2026Article
- Cell Fate Determination and Lineage Tracing: Technological Evolution and Multidimensional Applications.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Decoding cell fate: integrated experimental and computational analysis at the single-cell level.Bioinformatics (Oxford, England) · 2025Review
- DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity.Nature protocols · 2025Review
- Barcodes based on nucleic acid sequences: Applications and challenges (Review).Molecular medicine reports · 2025Review
- Advances in CRISPR-Cas9 in lineage tracing of model animals.Animal models and experimental medicine · 2025Review
- Clonal lineage tracing and transcriptomics of cortical progenitor populations reveal maintenance of differentiation potential.Stem cell reports · 2025Article
- Single-Cell Profiling of Lineages and Cell Types in the Vertebrate Brain.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Advancements in prospective single-cell lineage barcoding and their applications in research.Genome research · 2024Review
- Barcoding Notch signaling in the developing brain.Development (Cambridge, England) · 2024Article
- Barcoding Notch signaling in the developing brain.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.