In early mammalian development, timing is everything. For healthy development to occur, embryos follow the lead of oscillating genes, which turn on and off in precise cycles and trigger different development milestones. Oscillating genes are conductors keeping time in a symphony of growth.

Scientists at the Morgridge Institute for Research have created a way to study this process in humans, using human stem cells in the lab. According to the researchers, their “clock in a dish” opens new research avenues and provides a way to replicate developmental disorders to better understand their cause.

Reporting online in Cell Reports, the team describes growing human stem cells that are programmed into a very early state, within the first month of development. Then, using CRISPR technology, they edited a specific gene known to be connected to timing so it would illuminate when expressed.

The result: The cells growing in a dish produce a burst of color every five hours, precisely when those faithful oscillating genes are repeating their instructions. This is the first confirmation of the exact timing of oscillating genes in early human development.

Li-Fang Chu, a scientist in the lab of Morgridge and University of Wisconsin-Madison stem cell researcher James Thomson, says in a statement that most major oscillation findings to date have been with model organisms.

The project focuses on a specific phase of development called somitogenesis, or the development of body segments, which takes place around 20 days of development. It is a period when the 42-44 pairs of somites are forming, and they develop one after the other in a very precise pattern over a period of about two weeks.

Targeting this phase was valuable for two reasons, Chu says. First, it gives them a distinct time frame to study where there are recognizable physiological signatures, making it easier to match the genetic activity with the development. Second, a well-known genetic mutation occurs during this process that leads to a rare and debilitating disease.

The gene HES7 has been implicated in spondylocostal dysotosis (SCDO), where vertebrae improperly form and become fused together. Because past research highlighted the importance of HES7 to the segmentation clock, the lab made that gene the focus for CRISPR editing.

When HES7 is expressing normally in the experiment, the genes oscillate around every five hours as expected. But when introducing into HES7 a specific mutation associated with SCDO, the oscillation was completely disrupted. Essentially, the team recreated the conditions that cause SCDO and potentially other congenital skeletal defects.

“Like an airplane crash, we really don’t know what happened or what went wrong without the information in the black box,” Chu says. “I believe our system provides that black box.”