Cracking the code of developmental biology

March 23, 2017

Jay Shendure had the notion to put genetic barcodes on cells to track their development when he was just a young graduate student. Problem was, the technology to put that idea into action would not be developed for another decade. “At the time, I was encouraged to pick a different project that I could actually complete in a reasonable amount of time for my degree,” he says. “But the idea of taking that kind of global view and getting a comprehensive picture of what’s happening during development stayed in the back of my mind for years.”


The idea of lineage tracing—or recording how a single cell gives rise to complex organisms with thousands, millions or trillions of cells—dates back to the 1870s. But even as technologies graduated from dyes to more sophisticated techniques, researchers struggled to trace not only the lineage of cells, but how mature cells related to one another.

“Every one of us started out as a single cell that divided many times, ultimately giving rise to the highly organized mass of 40 trillion cells that is an adult human,” says Shendure. “That history, those relationships between the cells, is effectively an organism’s family tree. Understanding how that tree came to be is fundamental to developmental biology.”

Creating a lineage barcode 

With the advent of CRISPR gene editing technology and next generation sequencing, the idea that had been nagging at Shendure for years finally seemed possible to implement. Working in zebrafish and together with his collaborator Alexander Schier at Harvard University, his team inserted a “barcode” sequence of DNA into the genome of a fertilized zygote, and then also injected the Cas9 protein and guide RNAs that would allow the cell to generate unique mutations with every cell division. Having set the machine in motion, they stepped back and observed as the barcode they inserted into just one cell became more and more differentiated with each new generation of daughter cells.

When it came time to analyze the results, Shendure’s team used the patterns in the mature cells’ barcodes to trace back the origins of each cell. “If we see a change in the barcode that’s consistent across many of the cells, we can assume that the mutation took place earlier in the organism’s development, while rarer mutations probably happened later,” he explains. “We can use that information to learn not just about the progenitors of any given cell, but about the relationships between mature cells.”

Aside from its precision, part of the excitement around the technology—called GESTALT—is that it enables researchers to record development in the organism as it is actually happened. “Part of the reason there is so much uncertainty in the field of developmental biology is that we do so many experiments in a dish, which isn’t necessarily a perfect reflection of what really happens in the real biological context,” says Shendure. “This technology makes it possible to record the development of model organisms in vivo.”

Understanding development

Shendure sees the reconstruction of cell lineage histories not just as a means to an end, but as a valuable end in itself. To truly understand any organism, he says, we need to know what its cell lineage tree looks like, and we can then use that knowledge as a starting point for uncovering the molecular decisions that shape the tree’s creation.

“This generation of technologies that we’re developing will enable us to gain the same kind of global view on development that the Human Genome Project provided for our genes,” he says. “It won’t be an easy thing to bring this technology from where it is now to its fullest potential, but it has immense potential to crack open unanswered questions in developmental biology. Understanding cell lineage may unravel long-standing questions in human disease, such as how cancers originate and evolve, and how we recover brain function after strokes or traumatic injuries. The potential impact on human health is vast if this code can be unlocked.”

Read more about Jay Shendure's work as an Allen Distinguished Investigator on his project profile.