Distinct neuronal activity patterns induce different gene expression programs

Abstract

SUMMARYBrief and sustained neuronal activity patterns can have opposite effects on synaptic strength that both require activity-regulated gene (ARG) expression. However, whether distinct patterns of activity induce different sets of ARGs is unknown. In genome-scale experiments, we reveal that a neuron's activity-pattern history can be predicted from the ARGs it expresses. Surprisingly, brief activity selectively induces a small subset of the ARG program that that corresponds precisely to the first of three temporal waves of genes induced by sustained activity. These first-wave genes are distinguished by an open chromatin state, proximity to rapidly activated enhancers, and a requirement for MAPK/ERK signaling for their induction. MAPK/ERK mediates rapid RNA polymerase recruitment to promoters, as well as enhancer RNA induction but not histone acetylation at enhancers. Thus, the same mechanisms that establish the multi-wave temporal structure of ARG induction also enable different sets of genes to be induced by distinct activity patterns.

Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq

“…We next determined the genes specifically enriched in activated neurons in Ex17 ( n =129 genes, as compared to other Ex16) or Ex24 ( n = 157 genes, as compared to Ex25) neurons (Figure 3C). KEGG pathway analysis suggested that expression signatures of these two excitatory neuronal clusters are enriched for genes involved in the MAPK signaling pathway (adjusted P =5.74×10 −3 for E×17 and 8.14×10 −3 for Ex24), consistent with previous reports (Lacar et al, 2016; Tyssowski et al, 2017). We also observed heterogeneous expression patterns of ARGs (rapid IEGs: Fos and Egr1 ; delayed IEGs: Nr4a3 and Pcsk1 ) among nuclei in Ex24 ( Fos + : 53% in Ex24 versus 5.7% in Ex25; P =1.57E-71, Fisher’s exact test) and Ex17 ( Fos + : 55% in Ex17 versus 6.8% in Ex17; P =3.99E-31) excitatory neuronal clusters (Figure 3D and Table S2), in agreement with a continuum of transcriptional states of ARGs revealed by a recent analysis of Fos -positive neuronal nuclei isolated from adult mice exposed to a novel environment (Lacar et al, 2016).…”

“…Interestingly, despite variations in number of nuclei and sequencing depth among samples (Table S1), the small percentage of putatively activated neurons (Ex17: ~0.5%; Ex24: ~1.2% of all nuclei) was found in nearly all animals (Figure S4B), raising the possibility that neuronal activity-induced transcriptional states can be reproducibly captured by sNucDrop-Seq. We next performed gene set enrichment analysis (GSEA) of a recently curated list of ARGs induced by acute or prolonged neuronal activity (Tyssowski et al, 2017). This analysis indicated that both Ex17 (false-discovery rate [FDR]=0) and Ex24 (FDR=0) are significantly enriched for this set of ARGs (Figure 3B).…”

“…The first wave comprises primary response genes (PRGs, also called IEGs). The second wave comprises secondary response genes (SRGs), which require de novo translation for their induction and are likely to be regulated by PRG proteins (Tyssowski et al, 2017). Further analysis of top ranked PTZ-induced ARGs (separated into three groups: rapid PRG, delay PRG, and SRG) in each cluster indicates that rapid PRGs such as Fos and Egr1 are more likely to be detected in inhibitory neuronal clusters (Inh2 and Inh5), whereas delay PRGs (e.g.…”

“…The list of 172 ARGs was previously defined (Tyssowski et al, 2017). These ARGs were classified into 3 groups: rapid primary response genes (rapid PRG), delayed primary response genes (delayed PRG) and secondary response genes (SRG) based on the expression pattern across the time points in response to the KCl stimulation of cultured primary neurons (Tyssowski et al, 2017).…”

“…These ARGs were classified into 3 groups: rapid primary response genes (rapid PRG), delayed primary response genes (delayed PRG) and secondary response genes (SRG) based on the expression pattern across the time points in response to the KCl stimulation of cultured primary neurons (Tyssowski et al, 2017). For each cluster, only genes that were expressed in at least of 10% nuclei were considered and the expression matrix of those genes in each cluster was loaded into the GSEA analysis (www.broadinstitue.org/gsea/index.jsp) (Subramanian et al, 2005).…”