Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars

Nat Biotechnol. 2018 Jun;36(5):469-473. doi: 10.1038/nbt.4124. Epub 2018 Apr 9.


A key goal of developmental biology is to understand how a single cell is transformed into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the developmental origin of cells remains challenging. Here we present LINNAEUS (lineage tracing by nuclease-activated editing of ubiquitous sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas, and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CRISPR-Cas Systems / genetics*
  • Cell Lineage / genetics
  • Cell Tracking / methods
  • Computational Biology / methods
  • Gene Editing*
  • Genetic Engineering
  • Heart / growth & development
  • High-Throughput Nucleotide Sequencing / methods
  • Liver / growth & development
  • Liver / metabolism
  • Pancreas / growth & development
  • Pancreas / metabolism
  • Single-Cell Analysis / methods
  • Telencephalon / growth & development
  • Telencephalon / metabolism
  • Transcriptome / genetics*
  • Zebrafish / genetics*
  • Zebrafish / growth & development
  • Zebrafish / metabolism