An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

Sarah Bowling, Duluxan Sritharan, Fernando G. Osorio, Maximilian Nguyen, Priscilla Cheung, Alejo Rodriguez-Fraticelli, Sachin Patel, Wei Chien Yuan, Yuko Fujiwara, Bin E. Li, Stuart H. Orkin, Sahand Hormoz*, Fernando D. Camargo

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

82 Scopus citations

Abstract

Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Coupling of cell ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CRISPR array repair lineage tracing (CARLIN) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures associated with HSC activity without cell sorting.

Original languageEnglish
Pages (from-to)1410-1422.e27
JournalCell
Volume181
Issue number6
DOIs
StatePublished - 11 Jun 2020

Keywords

  • barcoding
  • hematopoiesis
  • lineage tracing
  • single cell
  • stem cells

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