Nathalie Guylaine Bérubé

ATR-X syndrome, caused by mutations in the ATRX gene, leads to intellectual disability and neurodevelopmental deficits, with previous mouse models implicating forebrain ATRX loss in cognitive impairment. However, the region-specific requirements of neuronal ATRX for cognitive function remain unclear. Here, we generated conditional knockout mice with predominant deletion of ATRX in hippocampal CA1 pyramidal neurons in both pure C57Bl/6J and hybrid C57Bl/6J + 129S2/Sv genetic backgrounds. Immunofluorescence confirmed efficient ATRX loss in CA1 neurons, with mosaic expression throughout other forebrain structures. Behavioral analyses revealed that T29-1 CaMKIIα-Cre ATRX knockout mice exhibited significant hypoactivity and increased anxiety traits, particularly in the open field, but retained normal hippocampal-dependent contextual fear memory and spatial learning and memory. In contrast, we confirmed that mice with robust forebrain-wide ATRX ablation in excitatory neurons (R1ag#5 CaMKIIα-Cre-mediated) displayed deficits in these cognitive domains. Our findings demonstrate that ATRX-related intellectual disability requires disruption of broader hippocampal or forebrain circuits to elicit cognitive impairments in learning and memory.

The online version contains supplementary material available at 10.1038/s41598-026-41476-5.

Mutations in the ATRX gene are a primary cause of alpha‐thalassemia intellectual disability X‐linked (ATRX) syndrome, which is characterized by intellectual disability, autism, and a range of brain structural abnormalities, including microcephaly. We previously showed that mice with conditional ATRX ablation in forebrain excitatory neurons display deficits in fear memory and autism‐related behaviors, with some effects exhibiting sexual dimorphism. In this study, we used high‐resolution magnetic resonance imaging (MRI) to systematically characterize brain structural changes associated with these behavioral abnormalities. Whole‐brain analysis revealed male‐specific microcephaly, while subregional analysis identified significant reductions in hippocampal structures and increased volume of the caudal cortex in mutant animals of both sexes. We also identified structural alterations in regions retaining ATRX expression, such as the thalamus, midbrain, cerebellum, and several fiber tracts. These findings suggest that ATRX loss disrupts the coordinated development of interconnected brain regions. Overall, our results implicate impaired cortico‐thalamic‐cerebellar connectivity as a potential neural substrate underlying the autistic‐like behaviors observed in this mouse model, providing new insights into the neurobiological basis of ATR‐X syndrome.

Astrocytes are increasingly recognized as active regulators of synaptic transmission and memory, yet the epigenetic mechanisms underlying their contribution to cognitive processes remain poorly defined. Here, we investigated the role of the chromatin remodeler ATRX in astrocytes by generating mice with inducible, astrocyte‐specific Atrx deletion (aiKO) using tamoxifen administration at postnatal days 10–12, resulting in ATRX loss in approximately half of hippocampal and cortical astrocytes. Transcriptomic profiling of hippocampal tissue at 1 and 3 months revealed differentially expressed genes, with early enrichment for cytoskeletal and immune pathways and later dysregulation of energy metabolism, ion transport, and synaptic gene sets. Electrophysiological recordings from CA1 pyramidal neurons in aiKO slices demonstrated increased neuronal excitability and decreased frequency of spontaneous excitatory postsynaptic currents, indicating non‐cell‐autonomous neuronal dysfunction. Morphological analysis identified a transient reduction in dendritic branching at 1 month and a selective loss of thin dendritic spines by 3 months, without changes in total dendrite length or overall spine density. Behaviorally, aiKO mice displayed normal locomotion, anxiety, and short‐term memory, but exhibited deficits in 24‐h novel object recognition and long‐term spatial memory in the Morris water maze. These findings demonstrate that ATRX‐mediated chromatin remodeling in astrocytes is essential for maintaining hippocampal transcriptional homeostasis, neuronal function, and long‐term memory. Our results highlight a critical role for astrocytic epigenetic regulation in cognitive processes and suggest that astrocyte dysfunction may contribute to the pathogenesis of ATR‐X syndrome and related intellectual disability disorders, underscoring the importance of targeting multiple cell types for therapeutic intervention.

The importance of chromatin-mediated processes in neurodevelopmental and intellectual disability disorders is well recognized. However, how chromatin dysregulation in glial cells impacts cognitive abilities is less well understood. Here, we demonstrate that targeted loss of the ATRX chromatin remodeler targeted to microglia leads to altered cell morphology, increased chromatin accessibility profiles, and de-repression of endogenous retroelements, triggering viral mimicry. In mice that lack ATRX in microglia, CA1 hippocampal neuron morphology and electrophysiological properties are affected, and the mice display specific behavioral deficits. These findings demonstrate that ATRX is required in microglia to preserve chromatin structure and maintain microglial homeostasis. Disruption of these functions elicits neuroinflammation and may contribute to the pathology of human neurological disorders caused by ATRX mutations.

Mutations in the ATRX gene are a primary cause of ATR-X syndrome, which is characterized by intellectual disability, autism, and a range of brain structural abnormalities, including microcephaly. We previously showed that mice with conditional ATRX ablation in forebrain excitatory neurons display deficits in fear memory and autism-related behaviors, with some effects exhibiting sexual dimorphism. In this study, we used high-resolution magnetic resonance imaging (MRI) to systematically characterize brain structural changes associated with these behavioral abnormalities. Whole-brain analysis revealed male-specific microcephaly, while subregional analysis identified significant reductions in hippocampal structures and increased volume of the caudal cortex in mutant animals of both sexes. We also identified structural alterations in regions retaining ATRX expression, such as the thalamus, midbrain, cerebellum, and several fiber tracts. These findings suggest that ATRX loss disrupts the coordinated development of interconnected brain regions. Overall, our results implicate impaired cortico-thalamic-cerebellar connectivity as a potential neural substrate underlying the autistic-like behaviors observed in this mouse model, providing new insights into the neurobiological basis of ATR-X syndrome. LAY SUMMARY: Changes in a gene called ATRX are known to affect brain development and are linked to intellectual disability and autism. In our previous work, we found that removing this gene early in brain development caused mice to show behaviors like those seen in people with autism. In this study, we used detailed brain scans to see if these behavioral changes were linked to differences in brain structure. We found that male mice without ATRX had smaller brains and bodies, while female mice did not show the same brain size reduction. However, both male and female mice had smaller areas of the brain important for memory and movement, and larger areas involved in thinking and sensing. We also saw changes in parts of the brain where ATRX was still present, suggesting that early changes in one area can affect how the whole brain develops. These findings help us understand how early disruptions in brain development might lead to autism-related behaviors.

Mutations in the chromatin-remodelling factor ATRX underlie syndromic ID and ASD, yet the contribution of microglial ATRX to early brain development remains unknown. We used a tamoxifen-inducible Cx3cr1-CreERT2 system to delete Atrx in microglia during the first postnatal week, achieving >90% recombination at one month of age. At both one and three months, ATRX-null microglia displayed a sustained increase in CD68-positive phagocytic foci and in Ki67+ proliferative microglia, but an unexpected ∼20% reduction in microglial density, despite only modest evidence of caspase-3-mediated apoptosis. A comprehensive behavioural battery conducted between three and six months revealed normal anxiety, locomotion, learning, memory, social interaction and sensory gating, coinciding with a decline in knockout efficiency to ∼45% in cortex and ∼75% in hippocampus, suggestive of microglial repopulation by ATRX-expressing cells. These findings demonstrate that perinatal loss of ATRX drives chronic microglial reactivity and turnover with no discernable effects on neurobehaviours, suggesting a developmental resilience of neural circuits to transient microglial dysregulation.

Astrocytes are increasingly recognized as active regulators of synaptic transmission and memory, yet the epigenetic mechanisms underlying their contribution to cognitive processes remain poorly defined. Here, we investigated the role of the chromatin remodeler ATRX in astrocytes by generating mice with inducible, astrocyte-specific Atrx deletion (aiKO) using tamoxifen administration at postnatal days 10–12, resulting in ATRX loss in approximately half of hippocampal and cortical astrocytes. Transcriptomic profiling of hippocampal tissue at one and three months revealed a progressive increase in differentially expressed genes, with early enrichment for cytoskeletal and immune pathways and later dysregulation of energy metabolism, ion transport, and synaptic gene sets. Electrophysiological recordings from CA1 pyramidal neurons in aiKO slices demonstrated increased neuronal excitability, reduced membrane capacitance, and decreased frequency of spontaneous excitatory postsynaptic currents, indicating non-cell-autonomous neuronal dysfunction. Morphological analysis identified a transient reduction in dendritic branching at one month and a selective loss of thin dendritic spines by three months, without changes in total dendrite length or overall spine density. Behaviorally, aiKO mice displayed normal locomotion, anxiety, and short-term memory, but exhibited deficits in 24-hour novel object recognition and long-term spatial memory in the Morris water maze. These findings demonstrate that ATRX-mediated chromatin remodeling in astrocytes is essential for maintaining hippocampal transcriptional homeostasis, neuronal function, and long-term memory. Our results highlight a critical role for astrocytic epigenetic regulation in cognitive processes and suggest that astrocyte dysfunction may contribute to the pathogenesis of ATR-X syndrome and related intellectual disability disorders, underscoring the importance of targeting multiple cell types for therapeutic intervention. Highlights: Astrocytic ATRX loss causes non-cell-autonomous neuronal hyperexcitability Inducing ATRX deficiency in astrocytes causes selective long-term memory deficits Dynamic transcriptomic changes reveal metabolic and synaptic pathway dysregulation

The importance of chromatin-mediated processes in neurodevelopmental and intellectual disability disorders is well recognised. However, how chromatin dysregulation in glial cells impacts cognitive abilities is less well understood. Here, we demonstrate that targeted loss of the ATRX chromatin remodeler in microglia alters chromatin accessibility profiles, leading to the de-repression of endogenous retroelements, triggering viral mimicry. Functionally, we find that ATRX microglial deficiency alters the electrophysiological properties of hippocampal neurons and causes deficits in object recognition and spatial memory. Overall, these findings demonstrate that ATRX is required in microglia to preserve chromatin structure and maintain microglial homeostasis. Disruption of these functions elicit neuroinflammation and cognitive deficits and potentially contribute to the pathology of human neurological disorders caused by ATRX mutations.

Background: ATRX is an ATP-dependent chromatin remodeling protein with essential roles in safeguarding genome integrity and modulating gene expression. Deficiencies in this protein cause ATR-X syndrome, a condition characterized by intellectual disability and an array of developmental abnormalities, including features of autism. Previous studies demonstrated that deleting ATRX in mouse forebrain excitatory neurons postnatally resulted in male-specific memory deficits, but no apparent autistic-like behaviours.Methods: We generated mice with an earlier embryonic deletion of ATRX in forebrain excitatory neurons and characterized their behaviour using a series of memory and autistic-related paradigms.Results: We found that mutant mice displayed a broader spectrum of impairments, including fear memory, decreased anxiety-like behaviour, hyperactivity, as well as self-injurious and repetitive grooming. Sex-specific alterations were also observed, including male-specific aggression, sensory gating impairments, and decreased social memory.Conclusions: Collectively, the findings indicate that early developmental abnormalities arising from ATRX deficiency in forebrain excitatory neurons contribute to the presentation of fear memory deficits as well as autistic-like behaviours.