•Neurons induce different genes in response to different extracellular stimuli.•This stimulation–transcription coupling is enabled by transcription regulation.•Recent genomic experiments begin to ...enable mapping of this coupling.•A neuron’s stimulation history can be inferred from its transcription state.
Neurons transcribe different genes in response to different extracellular stimuli, and these genes regulate neuronal plasticity. Thus, understanding how different stimuli regulate different stimulus-dependent gene modules would deepen our understanding of plasticity. To systematically dissect the coupling between stimulation and transcription, we propose creating a ‘stimulation–transcription coupling map’ that describes the transcription response to each possible extracellular stimulus. While we are currently far from having a complete map, recent genomic experiments have begun to facilitate its creation. Here, we describe the current state of the stimulation–transcription coupling map as well as the transcriptional regulation that enables this coupling.
A vast number of different neuronal activity patterns could each induce a different set of activity-regulated genes. Mapping this coupling between activity pattern and gene induction would allow ...inference of a neuron’s activity-pattern history from its gene expression and improve our understanding of activity-pattern-dependent synaptic plasticity. In genome-scale experiments comparing brief and sustained activity patterns, we reveal that activity-duration history can be inferred from gene expression profiles. Brief activity selectively induces a small subset of the activity-regulated gene program that corresponds to the first of three temporal waves of genes induced by sustained activity. Induction of these first-wave genes is mechanistically distinct from that of the later waves because it requires MAPK/ERK signaling but does not require de novo translation. Thus, the same mechanisms that establish the multi-wave temporal structure of gene induction also enable different gene sets to be induced by different activity durations.
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•Distinct durations of neuronal activity induce different gene expression profiles•Neuronal activity history can be inferred from gene expression•Brief activity induces a gene set defined by sensitivity to MAPK/ERK signaling•H3K27ac and eRNA induction are two separable steps of enhancer activation
Tyssowski et al. report that different durations of neuronal activity induce different gene expression profiles, enabling inference of past neuronal activity from gene expression data. Furthermore, they show that MAPK/ERK signaling partially establishes this activity-pattern-to-gene-induction coupling.
Optogenetics is widely used to control diverse cellular functions with light, requiring experimenters to expose cells to bright light. Because extended exposure to visible light can be toxic to ...cells, it is important to characterize the effects of light stimulation on cellular function in the absence of optogenetic proteins. Here we exposed mouse cortical cultures with no exogenous optogenetic proteins to several hours of flashing blue, red, or green light. We found that exposing these cultures to as short as 1 h of blue light, but not red or green light, results in an increase in the expression of neuronal activity-regulated genes. Our findings suggest that blue light stimulation is ill suited to long-term optogenetic experiments, especially those that measure transcription, and they emphasize the importance of performing light-only control experiments in samples without optogenetic proteins.
Despite dynamic inputs, neuronal circuits maintain relatively stable firing rates over long periods. This maintenance of firing rate, or firing rate homeostasis, is likely mediated by homeostatic ...mechanisms such as synaptic scaling and regulation of intrinsic excitability. Because some of these homeostatic mechanisms depend on transcription of activity-regulated genes, including
and
, we hypothesized that activity-regulated transcription would be required for firing rate homeostasis. Surprisingly, however, we found that cultured mouse cortical neurons from both sexes grown on multi-electrode arrays homeostatically adapt their firing rates to persistent pharmacological stimulation even when activity-regulated transcription is disrupted. Specifically, we observed firing rate homeostasis in
knock-out neurons, as well as knock-out neurons lacking the activity-regulated transcription factors AP1 and SRF. Firing rate homeostasis also occurred normally during acute pharmacological blockade of transcription. Thus, firing rate homeostasis in response to increased neuronal activity can occur in the absence of neuronal-activity-regulated transcription.
Neuronal circuits maintain relatively stable firing rates even in the face of dynamic circuit inputs. Understanding the molecular mechanisms that enable this firing rate homeostasis could potentially provide insight into neuronal diseases that present with an imbalance of excitation and inhibition. It has long been proposed that activity-regulated transcription could underlie firing rate homeostasis because activity-regulated genes turn on when neurons are above their target firing rates and include many genes that could regulate firing rate. Surprisingly, despite this prediction, we found that cortical neurons can undergo firing rate homeostasis in the absence of activity-regulated transcription, indicating that firing rate homeostasis can be controlled by non-transcriptional mechanisms.
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