Noise in the Vertebrate Segmentation Clock Is Boosted by Time Delays but Tamed by Notch Signaling

SUMMARY Taming cell-to-cell variability in gene expression is critical for precise pattern formation during embryonic development. To investigate the source and buffering mechanism of expression variability, we studied a biological clock, the vertebrate segmentation clock, controlling the precise spatiotemporal patterning of the vertebral column. By counting single transcripts of segmentation clock genes in zebrafish, we show that clock genes have low RNA amplitudes and expression variability is primarily driven by gene extrinsic sources, which is suppressed by Notch signaling. We further show that expression noise surprisingly increases from the posterior progenitor zone to the anterior segmentation and differentiation zone. Our computational model reproduces the spatial noise profile by incorporating spatially increasing time delays in gene expression. Our results, suggesting that expression variability is controlled by the balance of time delays and cell signaling in a vertebrate tissue, will shed light on the accuracy of natural clocks in multi-cellular systems and inspire engineering of robust synthetic oscillators.
In Brief Keskin et al. show that segmentation clock transcription levels display low amplitude and high heterogeneity. Clock gene expression variability is primarily driven by gene extrinsic sources, which is suppressed by Notch signaling. Gene expression noise increases along the posteroanterior axis. Spatial gradients of time delays contribute to the noise gradient along the axis.