Topographically organized dorsal raphe activity modulates forebrain sensory-motor computations and adaptive behaviors

Background:

The dorsal raphe nucleus (DRN), the vertebrate brain’s primary source of serotonin, governs behaviors such as mood regulation, sleep-wake cycles, and decision-making^1,2. Serotonin modulates synaptic plasticity, network oscillations, and internal states; roles mediated through diverse receptor subtypes expressed across the brain³. In mammals, the DRN is not a homogeneous structure but comprises distinct neuronal subpopulations. These subcircuits are thought to mediate different behavioral outputs, from reward processing to stress responses^4,5. However, how these molecularly-defined DRN populations dynamically encode sensory-motor information or regulate forebrain computations remains a major unresolved question.

Zebrafish, with their transparent brains and genetic tractability, have emerged as a powerful model for dissecting neuromodulatory circuits. In larvae, DRN neurons were shown to regulate motor adaptation by tracking action outcomes⁶ and modulate arousal states in response to ambient light^7,8. DRN activity is also linked to anxiety-like behaviors and social interactions, with ablation experiments implicating serotonergic signaling in threat recovery and habituation^9,10. These studies using larval zebrafish models focus on reflexive behaviors. Importantly, adult zebrafish studies often overlook developmental transitions. Juvenile zebrafish (3-4 weeks old) represent a critical intermediate stage, exhibiting cognitively complex behaviors like associative learning and social preference^11,12 alongside a forebrain that shares functional and anatomical homology with mammalian cortico-limbic systems, including the hippocampus, amygdala, and habenula^13,14,15.

The role of DRN inputs in shaping juvenile forebrain networks and their relevance to adaptive behaviors remains unexplored. Recent work in mice demonstrated that DRN neurons encode both external stimuli (e.g., rewards, aversive cues) and internal states (e.g., stress, hunger)^16,17 but technical limitations hinder large-scale recordings of DRN activity and projections in mammals. In contrast, zebrafish allow whole-brain imaging of genetically defined neurons and axons in awake, behaving animals, offering unparalleled resolution to map functional topography^18,19. This preprint leverages these advantages to investigate how spatially organized DRN ensembles process locomotion and sensory cues (Fig. 1), relay information to forebrain targets, and ultimately drive adaptive responses, a question central to understanding both basic neuromodulatory principles and their dysregulation in neuropsychiatric disorders.

 

 

Fig. 1 – Anatomical organization and functional clustering of dorsal raphe ensembles (a–h) illustrating the topographic organization of ongoing neuronal activity and high-fidelity ensemble dynamics in the dorsal raphe nucleus. Fig. 1 of the preprint, made available under a CC-BY-NC-ND 4.0 International license.

Key Findings:  

Topographic Organization:

The dorsal raphe nucleus (DRN) exhibits a spatially organized structure, with neurons grouped into distinct functional ensembles. These ensembles display correlated activity during rest and synchronized responses to sensory-motor stimuli such as locomotion, light, or vibrations. The proximity of neurons within these clusters correlates with their functional similarity, suggesting specialized subcircuits tailored to process specific types of information. This topographic arrangement likely enables the DRN to efficiently route diverse behavioral and sensory signals to downstream brain regions. The organization aligns with molecular diversity, as seen in Gad1b-expressing neurons, which occupy specific spatial niches within the DRN.

Sensory-Motor Encoding:

A majority of DRN neurons (60%) are dynamically modulated by locomotion, with 26% excited and 40% inhibited during movement. Smaller subsets respond to sensory cues, such as 7% reacting to light and 20% to vibrations, revealing specialized encoding roles. Notably, a genetically-defined anterior Gad1b-expressing neuronal cluster is predominantly inhibited during both locomotion and sensory events, distinguishing it from other DRN populations. This inhibition may reflect a regulatory mechanism to suppress competing behaviors during active states. Such sensory-motor integration positions the DRN as a hub for translating environmental and internal signals into adaptive neural activity.

Forebrain Projections:

DRN axons project to the forebrain with striking topographic specificity: locomotion-excited axons target anterior regions (e.g., olfactory areas), while inhibited axons innervate central zones (e.g., amygdalar homologs). These projections exhibit rapid covariation with forebrain neuron activity, suggesting direct excitatory or inhibitory coupling. The spatial segregation of axonal inputs allows distinct forebrain regions to receive tailored sensory-motor information. For instance, anterior projections may enhance exploratory behaviors, while central inputs modulate threat responses. This organization underscores the DRN’s role in dynamically shaping forebrain computations through precise anatomical and functional connectivity.

Why I highlight this preprint?

By bridging larval reflex studies and adult behavioral models, this work addresses a critical gap in our understanding of how neuromodulatory systems mature to support complex, state-dependent behaviors. It also builds on emerging evidence that DRN’s functional architecture once thought to broadcast serotonin diffusely is instead finely organized to route specific information streams to distinct forebrain regions, akin to a “switchboard” for sensory-motor integration^20,21. This preprint’s focus on juvenile zebrafish, a stage when forebrain-dependent behaviors first emerge, positions it to unravel how DRN-forebrain interactions evolve during development—a key step toward deciphering their roles in health and disease. Furthermore, what makes this study exceptional is its ability to redefine a brain region’s role by unifying anatomy, neural activity, and behavior with striking clarity. I was particularly impressed by how the discovery of a spatially distinct, locomotion-suppressing Gad1b+ population in the anterior dorsal raphe nucleus (DRN) overturns the outdated assumption of the DRN as a functionally uniform structure. Instead, it reveals specialized GABAergic subpopulations mirroring findings in mammals that fine-tune behavior, linking circuit architecture directly to functional outputs. Equally compelling is the causal demonstration of the DRN as a “conductor” of forebrain synchrony: ablating these neurons disrupts network-wide coordination, providing the first direct evidence for a theorized (but never proven) mechanism of brain-wide control. I also applaud the focus on juvenile zebrafish, a developmental “sweet spot” where forebrain-dependent behaviors emerge, offering insights into how neuromodulatory circuits mature.

Questions for the authors:

1. Your data show Gad1b+ DRN neurons are preferentially inhibited during sensory-motor events. Could this inhibition disinhibit downstream forebrain circuits to promote exploration? Or might these neurons actively suppress competing behaviors (e.g., freezing) during locomotion?
2. Gad1b is associated with GABA synthesis, yet DRN neurons are primarily serotonergic. Do Gad1b+ neurons co-release GABA and serotonin? If so, does this dual transmission explain their strong inhibitory coupling to forebrain neurons, or is their inhibition purely serotonergic via specific receptor subtypes?
3. DRN-ablated fish showed delayed exploration post-threat. How does the DRN integrate real-time sensory-motor signals to update forebrain circuits involved in risk-benefit assessments? Are specific forebrain regions (e.g., habenula or Dm) more dependent on DRN inputs for adaptive decisions?

References:

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Tags: #systemsneuroscience, zebrafish

doi: https://doi.org/10.1242/prelights.40460

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