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Tracing Cell Lineages with CRISPR/Cas

Jeffrey M. Perkel, Ph.D.

A new CRISPR-based barcoding technology enables researchers to follow the sequence of cell divisions that change a single fertilized cell into an organism. Learn more...

CRISPR barcoding enables researchers to trace cell lineages (1).

Metazoan organisms, such as fruit flies, zebrafish, and humans, arise from single cells. The question is, how?

Researchers have been looking for an answer for at least a century, but they’ve only succeeded once, when John Sulston used painstaking microscopy to tease apart the precise sequence of cell divisions and cell death required to turn a fertilized egg into an adult nematode worm. That approach would be tricky if not impossible to apply to more complex organisms. But a new method from Jay Shendure at the University of Washington and Alexander Schier at Harvard University could fill the gap.

Shendure and Schier designed a cellular barcode of 10 to 12 guide RNA binding sites separated by short spacers and then leveraged CRISPR/Cas9 genome editing to modify the barcode as cells divide. By sequencing the resulting barcodes and tracking how they change over time, the researchers can determine which cells arose from which progenitors. The team used their approach, dubbed Genome Editing of Synthetic Target Arrays for Lineage Tracing (GESTALT), to map lineage relationships in cell culture and in zebrafish embryos.

Surprisingly, the results suggest that adult organs in zebrafish arise from a relatively small number of progenitors. The vast majority of blood cells, for instance, come from just five ancestor cells. “I would have expected much greater diversity of cells giving rise to each organ,” Shendure said.

This isn’t the first barcoding method devised to track cellular lineages, noted Rong Lu from the University of Southern California. In 2014, for instance, researchers used the Sleeping Beauty transposase to trace hematopoiesis in mice [2]. Still, she said GESTALT could advance both regenerative medicine and stem cell research—for instance to work out the conditions required for differentiating induced pluripotent stem cells into defined cell types. “If we can identify the ancestors of a particular organ or tissue, we can determine the regulatory mechanisms that lead to these tissues or organs. And we can use those mechanisms to control regeneration or repair of tissue.”

The authors focused on early development, but in the future it should be possible to tweak the method to concentrate on specific tissue systems, such as bone, muscle, or brain.

According to Shendure, the team is now refining the method to allow for editing throughout development. In the meantime, however, the approach should be broadly extendable. “Any organism where you can do CRISPR/Cas9 [genome editing], you can do this,” he said.


1. McKenna, A., et al., “Whole organism lineage tracing by combinatorial and cumulative genome editing,” Science, May 26, 2016, doi:10.1126/science.aaf7907.

2. Sun, J., et al., “Clonal dynamics of native haematopoiesis,” Nature, 514:322–7, 2014.