2025 Theses Doctoral

Constitutive and Activity-Dependent Transcriptomic Profiles of SETD1A Disruption in Cortical Excitatory Neurons of a Schizophrenia-Risk Mouse Model

Apostolou, Panagiota

Schizophrenia is a complex neuropsychiatric disorder with strong genetic contributions, including rare, highly penetrant mutations in SETD1A, a lysine methyltransferase and core component of the Set/COMPASS complex. SETD1A plays a crucial role in histone H3K4 methylation, a chromatin mark associated with active transcription, yet how its disruption contributes to disease-relevant neuronal dysfunction remains incompletely understood. This thesis investigates the role of SETD1A in cortical excitatory neurons, a cell population implicated in schizophrenia, through an integrative approach combining chromatin profiling, transcriptomic analysis, and the characterization of gene regulation under both baseline and activity-dependent conditions.

In the first part of this study, I mapped SETD1A genomic binding sites in sorted cortical excitatory neurons from wild-type mice using CUT&Tag. Although Setd1a binding was predominantly enriched at promoter regions, a substantial fraction was also detected at enhancers marked by H3K4me1 and H3K27ac.

Transcriptomic analysis of Setd1a⁺/⁻ neurons revealed widespread dysregulation of gene expression, with downregulated genes enriched for metabolic processes and upregulated genes associated with synaptic signaling. These findings indicate that SETD1A orchestrates transcriptional programs related to metabolism and synaptic function through coordinated regulation at both promoters and enhancers. Notably, genes with Setd1a-bound enhancers were especially sensitive to haploinsufficiency, suggesting that enhancer-mediated regulation by Setd1a is dosage-dependent.

To investigate the full scope of Setd1a-dependent gene regulation and assess whether complete loss amplifies or alters these effects, I developed a conditional knockout strategy. Given that constitutive homozygous deletion of Setd1a leads to embryonic lethality, I generated a neuron-specific conditional knockout model enabling homozygous deletion specifically in cortical excitatory neurons.

In the second part of this study, I used this model to examine the effects of near-complete Setd1a loss. These mice exhibited pronounced hyperactivity and showed more extensive transcriptional dysregulation in excitatory neurons compared to heterozygous mutants. As in heterozygotes, promoter-associated downregulated genes were enriched for metabolic pathways, while enhancer-associated targets reflected changes in synaptic and developmental programs. A substantial subset of genes dysregulated in heterozygous neurons was also affected in homozygous mutants, supporting the idea that Setd1a haploinsufficiency is sufficient to disrupt a core set of directly regulated genes. This analysis also identifies a high-confidence set of disease-relevant targets that can guide future functional studies.

In the third part of this study, I employed a chemogenetic approach to induce neuronal activity and analyzed time-resolved transcriptional responses in Setd1a+/− and wild-type cortical excitatory neurons. In wild-type neurons, activity elicited a coordinated and temporally structured gene expression program. In contrast, Setd1a+/− neurons exhibited disrupted timing and specificity of activity-induced transcription. These neurons failed to appropriately downregulate synaptic genes and displayed exaggerated repression of metabolic genes, particularly at later time points. Mutant-specific responses were notably enriched for mitochondrial pathways, suggesting impaired energy homeostasis during neuronal activation. Furthermore, analysis of SETD1A targets dysregulated following activity induction revealed increased intergenic binding, implicating enhancer dysregulation as a key mechanism by which Setd1a deficiency disrupts activity-dependent transcriptional programs.

Collectively, this work uncovers a multifaceted role for SETD1A in regulating both baseline and activity-dependent transcription through promoter and enhancer elements in cortical excitatory neurons. Loss of SETD1A disrupts the balance between synaptic and metabolic gene programs, providing a mechanistic link between chromatin regulation and schizophrenia pathophysiology.