Abstract
Tracking the progeny of single cells is necessary for building lineage trees that recapitulate processes such as embryonic development and stem cell differentiation. In classical lineage tracing experiments, cells are fluorescently labelled to allow identification by microscopy of a limited number of cell clones. To track a larger number of clones in complex tissues, fluorescent proteins are now replaced by heritable DNA barcodes that are read using next-generation sequencing. In prospective lineage tracing, unique DNA barcodes are introduced into single cells through genetic manipulation (using, for example, Cre-mediated recombination or CRISPR–Cas9-mediated editing) and tracked over time. Alternatively, in retrospective lineage tracing, naturally occurring somatic mutations can be used as endogenous DNA barcodes. Finally, single-cell mRNA-sequencing datasets that capture different cell states within a developmental or differentiation trajectory can be used to recapitulate lineages. In this Review, we discuss methods for prospective or retrospective lineage tracing and demonstrate how trajectory reconstruction algorithms can be applied to single-cell mRNA-sequencing datasets to infer developmental or differentiation tracks. We discuss how these approaches are used to understand cell fate during embryogenesis, cell differentiation and tissue regeneration.
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The authors thank A. Alemany and J. Yeung for valuable feedback on the manuscript.
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C.S.B. researched data and wrote the manuscript. A.v.O. reviewed and edited the manuscript.
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Glossary
- Long-term haematopoietic stem cells
-
(LT-HSCs). Blood stem cells able to self-renew and differentiate into all types of mature blood cells.
- Primed cells
-
Differentiating cells with a determined cell fate.
- Lateral plate mesoderm
-
A subset of mesodermal tissue found in developing embryos that will form the body walls and circulatory system.
- Primitive wave of haematopoiesis
-
A process by which the embryo generates transient haematopoietic cells, which are necessary for embryonic development.
- Definitive wave of haematopoiesis
-
A process by which definitive adult haematopoietic stem cells are generated during embryogenesis.
- Dome stage
-
A developmental stage of zebrafish embryos that is reached at 4.3 h of development.
- Nuc-seq
-
RNA-sequencing technology for nuclear RNA capture from frozen tissue samples.
- Minimum spanning tree
-
The shortest way to connect all edges of a graph.
- Pseudotime
-
A quantitative measure of biological progression through a process such as cell differentiation.
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Baron, C.S., van Oudenaarden, A. Unravelling cellular relationships during development and regeneration using genetic lineage tracing. Nat Rev Mol Cell Biol 20, 753–765 (2019). https://doi.org/10.1038/s41580-019-0186-3
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DOI: https://doi.org/10.1038/s41580-019-0186-3
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