Promoter Selection and Smith-Magenis Syndrome Protein Retinoic Acid Induced-1 in Neuronal Activity-Dependent Transcription

Abstract

The brain adapts to the environment by converting signals of neural activity into altered synaptic connections. Long-term reshaping of synapses depends upon neural activity-dependent transcription. Activity-dependent transcription, in turn, requires proper packaging of the DNA through chromatin regulation. Genes encoding chromatin regulators, transcription factors, and synaptic proteins are all associated with autism spectrum conditions and rare intellectual disabilities. Such neurodevelopmental conditions may result, then, from a convergence on similar molecular pathways, such as activity-dependent synaptic plasticity. Indeed, forms of synaptic plasticity such as long-term potentiation/depression and synaptic scaling are known to require specific synaptic proteins and transcription factors. However, the roles of chromatin regulating proteins in these processes remain poorly understood. In part, this is due to the difficulty of examining how chromatin regulators directly guide activity-dependent transcription. Chromatin regulators’ direct effects are obscured by the commonly used technique of seeking differentially expressed genes from steady-state mRNA profiles. Furthermore, compared to transcription factors, chromatin regulators can have fewer dramatic gene-specific effects on transcription. Therefore, I used the nascent RNA sequencing method BrU-seq and adapted RNA-seq analyses to examine chromatin regulator function in the context of activity-dependent transcription associated with synaptic scaling. I then revealed a role for the Smith-Magenis Syndrome protein Retinoic Acid Induced-1 (RAI1) as a regulator of activity-dependent transcription and synaptic strength in the baseline and low-activity states of neurons. In a distinct project, I found that neural activity shifts alter not only gene expression, but also gene promoter selection. I determined that multi-promoter genes make up nearly 10% of expressed genes in neuronal cultures, and that neuronal activity guides differential promoter usage in ~10% of them. I also observed differential promoter/transcription start site usage in vivo in physiological models of neuronal activity induction and found evidence of excitatory-neuron-specific promoter switching. Differential promoter usage predominately predicts altered N-terminal protein sequences of synaptic and phosphodiesterase family genes. Promoter-specific isoforms of the phosphodiesterase PDE2A revealed differential organelle-targeting and altered electrophysiological properties, suggesting promoter usage can regulate subcellular protein localization and synaptic function. In sum, these two projects detail new concepts of activity-dependent transcription and synaptic homeostasis that may be critical to human neurodevelopment and mature brain function.