Differentiation trajectories of the Hydra nervous system reveal transcriptional regulators of neuronal fate

The small freshwater cnidarian polyp Hydra vulgaris uses
adult stem cells (interstitial stem cells) to continually replace neurons
throughout its life. This feature, combined with the ability to image the
entire nervous system (Badhiwala et al., 2021; Dupre &
Yuste, 2017) and the availability of gene knockdown
techniques (Juliano, Reich, et al., 2014; Lohmann et al., 1999;
Vogg et al., 2022), makes Hydra a tractable model for
studying nervous system development and regeneration at the whole-organism
level. In this study, we use single-cell RNA sequencing and trajectory
inference to provide a comprehensive molecular description of the adult
nervous system. This includes the most detailed transcriptional
characterization of the adult Hydra nervous system to
date. We identified eleven unique neuron subtypes together with the
transcriptional changes that occur as the interstitial stem cells
differentiate into each subtype. Towards the goal of building gene
regulatory networks to describe Hydra neuron
differentiation, we identified 48 transcription factors expressed
specifically in the Hydra nervous system, including many that are
conserved regulators of neurogenesis in bilaterians. We also performed
ATAC-seq on sorted neurons to uncover previously unidentified putative
regulatory regions near neuron-specific genes. Finally, we provide
evidence to support the existence of transdifferentiation between mature
neuron subtypes and we identify previously unknown transition states in
these pathways. Altogether, we provide a comprehensive transcriptional
description of an entire adult nervous system, including differentiation
and transdifferentiation pathways, which provides a significant advance
toward understanding mechanisms that underlie nervous system regeneration.