In preprints: robust segmentation clock outputs via cell cycle and synthetic coupling Free

The segmented body plan of vertebrates becomes apparent during development, when two bilaterally symmetrical rows of somites emerge along the body axis. This process, known as somitogenesis, occurs sequentially as new somites separate at regular intervals from the precursor tissue, the pre-somitic mesoderm (PSM). Somitogenesis is remarkably robust and consistent, with somite size, number and symmetry being highly regular across individuals. This robustness arises from its complex signalling network, operating at multiple scales (reviewed by Oates et al., 2012). At the cellular level, the cell-autonomous oscillatory gene expression of the segmentation clock controls the timing of somitogenesis. Intercellular coupling synchronises neighbouring cells, producing tissue-level waves of gene expression that interact with morphogen gradients and coordinate the position, timing and size of somite formation. Despite extensive research, understanding how the crosstalk between different signalling modules ensures robust morphogenetic outcomes has remained challenging due to the complexity of the system. Now, two preprints have shed light on the mechanisms regulating somitogenesis through cell- and tissue-level couplings.

In the first preprint, Oostrom and colleagues (Oostrom et al., 2025 preprint) investigated the long-suspected link between somitogenesis and the cell cycle. By characterising the cell cycle dynamics in mouse embryo tails, they revealed that all cells throughout the PSM are actively proliferating with a cell cycle duration that is five times slower than the segmentation clock. This is in contrast with previous observations supporting the existence of a defined proliferative region at the posterior end of the embryonic tail (Cambray and Wilson, 2002; Mathis and Nicolas, 2000). Interestingly, cells at the G1-S transition formed spatially defined patterns, indicating regulated control of cell cycle entry within the PSM. The authors explored this further by simultaneously tracking the cell cycle and the segmentation clock oscillations in ex vivo cultured embryo tails. Aligning the segmentation clock tracks with the G1-S transitions revealed a phase correlation among the two, but only when analysing cells in the posterior and anterior PSM separately. This distinction is consistent with earlier findings showing that phase relationships among segmentation clock oscillators shift along the anterior-posterior axis (Sonnen et al., 2018). The authors then probed this link between proliferation and the segmentation clock by functionally modulating the oscillations in the PSM. Using a microfluidic device, they applied periodic drug pulses to entrain the segmentation clock. Remarkably, G1-S transitions were more likely to occur in phase with the entrained oscillations, suggesting that the segmentation clock and cell cycle progression are coupled. To understand the implications of this coupling, the authors developed a theoretical model of somitogenesis, in which synchronisation between cell cycle entry and the segmentation clock resulted in more uniform tissue growth and somite formation by evenly diluting morphogen gradients. They tested their predictions experimentally by inhibiting proliferation in mouse tails. Surprisingly, cell cycle inhibition did not affect tissue size within the experimental time frame, suggesting that proliferation was not the main contributor of tissue growth. Instead, morphogen gradients expanded within the PSM, leading to a larger oscillating field, disrupted somite formation, and altered size scaling. Taken together, Oostrom and colleagues propose a model in which cellular proliferation plays a crucial role in shaping morphogen gradients to regulate somite formation. The local coupling between the segmentation clock and the cell cycle ensures an even distribution of proliferating cells, maintaining proper segmentation at the tissue level. A similar scaling role for cell proliferation has been observed in other developing tissues, such as the Drosophila wing disc, where morphogen-induced local cell division enables gradient scaling (Averbukh et al., 2014). Here, the coupling between dynamic signalling oscillations and the cell cycle reveals a previously unappreciated mechanism for tissue scaling during somitogenesis.

In the second study, Isomura and colleagues (Isomura et al., 2024 preprint) engineered a synthetic optogenetic signalling system to investigate cell-to-cell communication during segmentation clock synchronisation. In PSM cells, intercellular signalling via the Delta-Notch pathway allows synchronised oscillations, generating tissue-level waves of gene expression. Inhibiting Notch signalling or knocking out the Delta ligand results in dampened and uncoordinated oscillations (De Angelis et al., 1997; Tsiairis and Aulehla, 2016). However, identifying the minimal cell–cell coupling mechanism required for synchronising oscillatory signals across cells has remained challenging due to the complexity of the Notch signalling. To overcome this, the authors developed a synthetic minimal alternative. By replacing the extracellular domains of the Delta-Notch molecules with synthetic proteins, they created an optogenetic sender-receiver system. In this setup, light-sensitive sender cells activate synthetic ligand expression upon blue light illumination, while light-insensitive receiver cells express receptors that, when triggered by the ligand, induce luciferase gene expression. Cyclic blue light stimulation of a co-culture containing both cell types resulted in luminescence oscillations, suggesting that oscillatory information can be transferred from sender to receiver cells. Interestingly, the ability of the system to relay oscillatory signals was highly dependent on the properties of the synthetic ligand. The authors reported that modifying the intracellular domain of the ligand affected the speed of signal transmission, with Delta ligand domains showing the best responses. Similarly, altering the extracellular domain interaction strength affected the amplitude of the resulting oscillatory signal. To test the system further, the authors rewired the natural synchronisation system of PSM cells by integrating the synthetic ligand–receptor pair into the Notch signalling pathway. This synthetic minimal system was able to partially rescue segmentation clock oscillations and wave dynamics in Delta-null in vitro-derived PSM cells and organoids. Overall, Isomura and colleagues developed a tuneable cell–cell coupling system capable of propagating oscillatory information across cells and restoring the synchrony of the segmentation clock in Delta/Notch-deficient conditions. This tool will be highly valuable for dissecting the role of specific protein domains in the temporal regulation of signal transmission.

Together, these two preprints provide new insights into cellular- and tissue-level coupling during somitogenesis, with one uncovering mechanisms that ensure robust segmentation outputs and the other offering powerful tools for studying cell–cell communication. Local regulation through cell proliferation and notch signalling plays a key role in modulating tissue-wide morphogenetic behaviours. These principles may also govern other developing tissues exhibiting signalling oscillations, such as neural stem cells (Maeda et al., 2023). Interestingly, both the segmentation clock and the cell cycle are oscillatory systems, suggesting that periodic signalling inputs could be particularly effective in coordinating cell cycle entry. It would be interesting to investigate how the architecture of different signalling circuits influences their ability to modulate one another. For this, advances in synthetic biology provide an unprecedented opportunity to dissect these coupling mechanisms. By rewiring natural gene regulatory networks with synthetic alternatives, we can probe the minimal components required for effective coupling. Such precise descriptions will be essential for understanding the interplay between signalling dynamics, scaling and robustness in developmental systems.