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Science. 2016 Jul 29;353(6298):aaf7907. doi: 10.1126/science.aaf7907. Epub 2016 May 26.

Whole-organism lineage tracing by combinatorial and cumulative genome editing.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
2
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
3
Department of Genome Sciences, University of Washington, Seattle, WA, USA. Department of Pathology, University of Washington, Seattle, WA, USA.
4
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA. Center for Brain Science, Harvard University, Cambridge, MA, USA. The Broad Institute of Harvard and MIT, Cambridge, MA, USA. FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA. shendure@uw.edu schier@fas.harvard.edu.
5
Department of Genome Sciences, University of Washington, Seattle, WA, USA. Howard Hughes Medical Institute, Seattle, WA, USA. shendure@uw.edu schier@fas.harvard.edu.

Abstract

Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable and that thousands of lineage-informative barcode alleles can be generated. By sampling hundreds of thousands of cells from individual zebrafish, we find that most cells in adult organs derive from relatively few embryonic progenitors. In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease.

Comment in

PMID:
27229144
PMCID:
PMC4967023
DOI:
10.1126/science.aaf7907
[Indexed for MEDLINE]
Free PMC Article

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