Tiny Genetic Fragments Play a Big Role in Regulating Brain Activity

Very short fragments of neuronal genes, known as microexons, are essential for telling the brain when to rest. 

A new study from Pompeu Fabra University and the Center for Genomic Regulation has shown that the absence of these microexons increases brain activity and disrupts sleep in zebrafish models. 

As neuronal hyperactivity is associated with neurodevelopmental disorders such as autism and schizophrenia, this finding could help improve understanding of an underlying mechanism behind symptoms of these conditions. 

Central nervous system activation is a survival mechanism 

Being able to adapt to external and internal stimuli is crucial for survival. The regulation of arousal—the state of central nervous system activation—ensures a balance between rest and activity and enables appropriate behavioral responses. Not enough arousal results in reduced responsiveness or drowsiness, and too much can lead to heightened activity, insomnia, and sensory hypersensitivity.  

Such arousal states are largely evolutionarily conserved across the animal kingdom, from fruit flies and zebrafish to humans. 

Neuromodulatory systems control and maintain arousal states in vertebrates, transmitting signals through diverse G protein-coupled receptors (GPCRs) that modulate cyclic adenosine monophosphate (cAMP) levels to engage cellular responses. 

Activation of the cAMP—cAMP-dependent protein kinase (PKA)—cAMP response element–binding protein (CREB) pathway promotes the expression of activity-dependent genes, helping to fine-tune synaptic connections that maintain the balance of arousal levels. Post-transcriptional modification of mRNA encoding GPCRs or downstream effector proteins may also shape neuronal responsiveness and arousal control. 

Alternative splicing, where multiple transcripts are generated from a single gene, is an important element of post-transcriptional control, as it enables greater protein diversity. Levels of alternative splicing are particularly high in the brain. 

During neurodevelopment, microexons can be spliced into mRNA, influencing the functional properties of the final protein. 

 

In the brain, the subtle changes to proteins from microexon inclusion can influence synapse formation and axon guidance, potentially altering neural circuits and transmission. 

The impact of microexon inclusion on arousal 

To assess how microexon splicing affects arousal, the researchers used zebrafish models that lacked a critical domain for microexon inclusion.

 

Behavioral profiling, whole-brain activity imaging, and transcriptomic assays were combined to connect changes to microexon splicing with neuronal activity and behavior.

 

Zebrafish with altered microexon splicing displayed a hyperactivity phenotype, with disrupted sleep and intense responses to external stimuli, indicating that arousal was dysregulated. 

“They sleep less frequently and for shorter periods, and it takes longer for them to fall asleep,” explained Dr. Tahnee Mackensen, first author of the study. 

Imaging of neural activity found an increase in overall signaling events, as well as an increase in signaling frequency and amplitude in mutant zebrafish compared to wild type, illustrating a hyperaroused brain state.

Splicing alterations were noted to elevate cAMP levels, dysregulating the cAMP-PKA-CREB pathway and leading to neuronal hyperactivity. 

“The fish with [microexon splicing] abnormalities are in a state of permanent overexcitation,” Mackensen said. 

A cross-species finding 

Previous research by the same team identified similar behavioral and neuronal changes in flies with altered microexon splicing, indicating that the role of microexons in regulating arousal may be conserved across species.

“We know that the alteration of these microexons causes sleep deprivation in fish and flies,” explained Dr. Manuel Irimia, director of the research. He added: “It is likely that this mechanism is conserved in mammals, including humans, although perhaps not in exactly the same way.” 

In humans, disruption in microexon regulation has been reported in autism and schizophrenia, conditions in which sleep disturbances and hypersensitivity are common. 

“Although they are not the cause of the disease, we know that changes in protein production can contribute to the symptoms of the disorder,” Irimia acknowledged. 

In the work in zebrafish, the researchers showed that reducing cAMP levels through chemical inhibition returned the activity of mutant fish to a normal level, confirming cAMP’s central role in driving activation behavior. 

“In this sense, it is plausible to study whether the treatment to restore the activation state in fish also corrects or alleviates symptoms in other species,” said Irimia. 

While the work uncovered neuronal microexons as a key modulator of arousal via cAMP signaling, it also identified genetic compensatory mechanisms when microexon splicing is altered, meaning the relationship between microexon mis-splicing and hyperarousal remains correlational, rather than causative.

The upstream trigger of the cAMP signaling dysregulation is also yet to be determined, although the authors suggest that additional targeted perturbation studies could help elucidate candidate mechanisms. 

Reference: Mackensen T, Iñiguez LP, Soares Mullen T, et al. Neuronal microexons modulate arousal via the cAMP-PKA-CREB pathway in zebrafish. Sci Adv. 2026;12(25):eady8291. doi: 10.1126/sciadv.ady8291 

This article is a rework of a press release issued by Pompeu Fabra University. Material has been edited for length and content.