bioRxiv2026
The development and physiology of neurons rely on their microtubule organization, which is characterized by plus-end-out oriented microtubules in the axon and a mix of plus-end-out and plus-end-in oriented microtubules in dendrites. This orientational pattern is established early in neuronal development and is tightly linked to axon-dendrite differentiation. Even though multiple potentially relevant mechanisms have been proposed, fundamental questions remain: How does the microtubule organization in neurons emerge, and how does a neuron develop a single axon and multiple dendrites? Here, we address these questions at two distinct, complementary levels: at a higher level by proposing a conceptual framework, in which we classify mechanisms into three categories based on how they contribute to the microtubule organization: orientational bias, parallel amplification, and polarization; at a lower level we build a biophysical model that incorporates multiple mechanisms of microtubule dynamics in a neuron, from which, using analytical calculations and simulations, we derive insights into the emergence of microtubule organization in developing neurons. We show that geometrical effects alone can confer a bias in microtubule orientation. Parallel amplification then enhances the resulting polarity. Coupling multiple neurites to a common cell body that serves as a shared reservoir of resources allows for a polarization mechanism that ensures that the microtubule organization of one neurite becomes axonal while all others are dendritic. This framework unifies diverse molecular observations and yields experimentally testable predictions about microtubule self-organization in early neuronal development. Author summaryNeurons communicate through long protrusions called neurites, which are of two types: dendrites, which receive signals, and axons, which send signals. Their development relies primarily on microtubules, which are polar filaments with two distinct ends, known as the plus and minus ends. Microtubules self-organize into functional architectures that are significantly different between axons and dendrites. In axons, all microtubules point their plus end away from the cell body, whereas in dendrites, they point either towards the cell body or have mixed orientations depending on the species. This orientation guides intracellular transport by motors and is closely linked to whether a neurite develops into an axon or a dendrite. Despite decades of research identifying individual mechanisms, the bigger picture behind the emergence of microtubule orientation in neurons remains unclear. Here, we construct a conceptual framework and a biophysical model to identify the principles underlying the emergence of microtubule orientation in developing neurons. Our conceptual framework provides a high-level perspective on how individual mechanisms influence microtubule organization in neurites. In our concrete biophysical model, we study a selection of mechanisms to gain specific, quantitative insight into the organizational process. We propose a minimal model of a neuron that exhibits neuronal polarization, giving rise to a single axon-like neurite and multiple dendrite-like ones, consistent with experimental observations. This in silico neuron helps to explain how neurons break symmetry during development and provides a systematic way to generate and test new hypotheses about neuronal polarity.