Genomic and Proteomic Regulation of Activity-Dependent Neuronal Function

Abstract

As postmitotic cells, neurons face the unique challenge of dynamically responding to changing environments while simultaneously stably encoding information over the lifetime of an animal. To accomplish this, neurons utilize an intricate system of molecular mechanisms. Much of this regulatory program is activated in neurons in response to experience—neuronal activity triggers calcium influx, in turn transiently activating signaling cascades that rapidly induce diverse downstream pathways, including post-translational protein modifications, transcriptomic regulation, and synaptic remodeling. Here, we present three studies that investigate distinct molecular mechanisms involved in activity-dependent neuronal regulation. We begin by examining transcriptomic regulation through the lens of the immediate early gene, NR4A1. Using biochemical techniques, we discover that the COMPASS complex—a histone H3K4 methyltransferase and transcriptional regulator—assembles together with NR4A1 in neurons. In NR4A1 knockout mouse brains, we find that chromatin binding of the COMPASS complex is reduced at NR4A1 binding sites near genes that regulate dendritic spines, suggesting that NR4A1 facilitates COMPASS complex recruitment and subsequent gene activation for neuronal function. Consistent with this finding, we observe that distal regulatory elements have altered accessibility in NR4A1 knockout mice, suggesting dysregulation by the COMPASS complex. Furthermore, RNA-sequencing of the hippocampus reveals that loss of NR4A1 leads to downregulation of numerous synaptic regulatory genes and ion channels. Finally, we demonstrate that NR4A1 deletion reduces Sag current in CA1 pyramidal neurons, consistent with the observed transcriptomic changes and indicative of disrupted neuronal function in the absence of NR4A1. In our second study, we look at the impact of protein phosphorylation on brain function and gene expression. Here, we show that MeCP2 is phosphorylated at four residues in the mouse brain (S86, S274, T308, and S421) in response to neuronal activity and generate a quadruple knock-in (QKI) mouse line in which all four activity-dependent sites are mutated to alanines to prevent phosphorylation. Electrophysiological recordings from the retinogeniculate synapse of QKI mice reveal that while synapse elimination is initially normal at P14, it is significantly compromised at P20. We thus propose a model in which activity-induced phosphorylation of MeCP2 is critical for the proper timing of retinogeniculate synapse maturation during the early postnatal period. Lastly, we demonstrate that neuronal activity-dependent phosphorylation events primarily occur in disordered regions of proteins, where they control structural transitions and modulate condensation dynamics in the nucleus. We focused on one of these events, the phosphorylation of histone methyltransferase SETD2, and found that disrupting activity-dependent and condensation-modulating phosphorylation of SETD2 impairs histone methylation, RNA splicing programs, neuronal excitability, and leads to changes in social behavior akin to autism-like behavior in mice.