A New Genome-Editing Technique

A recent study uses CRISPR technology to mark cells with a genetic barcode that helps track their development and reconstruct their lineages.

by Jalwa Afroz

Developmental biology explores how cells differentiate from a fertilized egg into a complex multicellular organism. Although the idea of marking cells to track their development is not new, scientists at Harvard University and the University of Washington developed a CRISPR genome-editing system that offers far more specificity and versatility by tracing cells with fluorescent proteins. In order for a technology to trace complex cell lineages, it must incrementally mark every unique cell and its descendants over many divisions, while at the same time, not interfere with normal development. These markers must also be irreversible, so they can accumulate over time instead of fading away before they can be traced and reconstructed into lineage trees.

This CRISPR genome-editing system, called the Genome Editing of Synthetic Target Arrays for Lineage Tracing (GESTALT), targets ten short sequences of DNA and randomly cuts them. As the cells try to repair the cuts, some deletions and insertions are formed in their DNA. Scientists can then sequence these areas, determine the precise order of nucleotides within the DNA, and understand how the cells relate to each other. GESTALT is intricate because although only one sequence in a single cell may be cut, as it divides its daughter and granddaughter cells may be cut in additional locations. By tracing how these changes in cell generations accumulate, scientists can observe how cells relate to each other. For example, the more closely related cells are, the more similar their mutated DNA barcodes are.

Researchers that developed GESTALT demonstrated its effectiveness in cell cultures and zebrafish Donio rerioi. The cell culture results showed that the diverse edits successfully accumulated to allow informative cell lineage tracing. Likewise in zebrafish, researchers were able to show hundreds to thousands of uniquely edited barcodes per animal and infer lineage relationships by looking for shared mutations. For example, researchers showed that the majority of cells in each organ are derived from a small number of progenitor cells. However, there are limitations to this method: the maximum amount of 100 colors is not enough to show all the cell lineages in complex organisms. Further optimization of GESTALT can accurately record various types of information and history in living cells.



  1. McKenna, et al., Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, 462-473 (2016). doi:10.1126/science.aaf7907.

Image retrieved from: http://en.hdbuzz.net/038


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