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

Lianshun Xie1,2, Hengxin Liu2,3, Zhiwen You1,2

  • 1Institute of Neuroscience, Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.

Nature Methods
|July 17, 2023
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Summary

Researchers developed CRISPR editing-based lineage-specific tracing (CREST) to map brain cell development. This method revealed progenitor archetypes and distinct neuronal lineages in the developing mouse brain, offering insights into neural specification.

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Area of Science:

  • Neuroscience
  • Developmental Biology
  • Genetics

Background:

  • Mapping single-cell lineages in the brain is crucial for understanding neural development.
  • Existing methods may have limitations in comprehensively tracing cell fates.

Purpose of the Study:

  • To develop and apply a novel CRISPR editing-based method for lineage-specific tracing (CREST) in mice.
  • To construct a detailed spatiotemporal lineage map of the developing mouse ventral midbrain (vMB).
  • To associate progenitor cell transcriptomes with their differentiation potentials.

Main Methods:

  • Development of CRISPR editing-based lineage-specific tracing (CREST).
  • Application of snapshotting CREST (snapCREST) for lineage landscape construction.
  • Utilizing progenitor and derivative associating CREST (pandaCREST) for transcriptome-differentiation potential association.

Main Results:

  • Identified six progenitor archetypes and three distinct clonal lineages in the developing vMB.
  • Revealed multiple origins of dopaminergic neurons.
  • Demonstrated that transcriptome-defined progenitor types contain heterogeneous progenitors with distinct clonal fates.

Conclusions:

  • The CREST method enables comprehensive single-cell lineage analysis in the developing brain.
  • Findings provide new insights into the molecular programs governing neural specification.
  • The study highlights the heterogeneity within progenitor populations and their diverse differentiation potentials.