Intracellular Zn²⁺ transients modulate global gene expression in dissociated rat hippocampal neurons

Zinc (Zn²⁺) is an integral component of many proteins and has been shown to act in a regulatory capacity in different mammalian systems, including as a neurotransmitter in neurons throughout the brain. While Zn²⁺ plays an important role in modulating neuronal potentiation and synaptic plasticity, little is known about the signaling mechanisms of this regulation. In dissociated rat hippocampal neuron cultures, we used fluorescent Zn²⁺ sensors to rigorously define resting Zn²⁺ levels and stimulation-dependent intracellular Zn²⁺ dynamics, and we performed RNA-Seq to characterize Zn²⁺-dependent transcriptional effects upon stimulation. We found that relatively small changes in cytosolic Zn²⁺ during stimulation altered expression levels of 931 genes, and these Zn²⁺ dynamics induced transcription of many genes implicated in neurite expansion and synaptic growth. Additionally, while we were unable to verify the presence of synaptic Zn²⁺ in these cultures, we did detect the synaptic vesicle Zn²⁺ transporter ZnT3 and found it to be substantially upregulated by cytosolic Zn²⁺ increases. These results provide the first global sequencing-based examination of Zn²⁺-dependent changes in transcription and identify genes that may mediate Zn²⁺-dependent processes and functions.