CLOK: a chemigenetic multicolor labeling system to visualize neuronal birthdate and circuit integration

Abstract Understanding how neurons integrate into developing circuits and contribute to functional activity is essential for decoding brain development and plasticity. However, current methods to study neuronal integration often suffer from low throughput, limited spatiotemporal resolution or invasive procedures. To overcome these challenges, here we present CLOK, an in vivo birthdate-labeling strategy based on HaloTag technology and its broad palette of fluorescent ligands. We show that CLOK enables precise color-coding of neurons and their subcellular structures by birthdate and allows tracking of functional maturation of newborn neurons in the developing zebrafish visual and motor systems, revealing distinct maturation trajectories of early- and late-born neurons. We further demonstrate the versatility of this approach by coupling it to optical tools enabling age-specific multicolor calcium and voltage imaging, as well as optogenetic manipulation. Altogether, CLOK provides a powerful and flexible tool for optical interrogation of neuronal circuit maturation in a growing and behaving vertebrate.