A comparative transcriptomics approach for unveiling gene expression networks of activity-driven neuronal stimulation and plasticity

Abstract

Activity-dependent gene expression is a well-known mechanism of Hebbian plasticity. Despite a compelling body of evidence demonstrating the necessity of de novo transcription and protein synthesis for several forms of neuronal plasticity, relatively little is known about the genome-wide events that are elicited upon neuronal stimulation. We have used last-generation microarrays in combination with lentivirus-mediated gene transfer in primary cultured hippocampal neurons to systematically characterize and compare the transcriptomes of four major regulators of activity-dependent transcription: CREB, SRF, EGR1, and FOS. In addition, we have performed profiling experiments in hippocampal neurons under different stimulation conditions. Our results indicate that these four transcription factors orchestrate convergent biological processes through the regulation of largely non-overlapping gene expression programs, reveal their individual and collective contribution to different activity-driven gene programs, and reinforce the widely accepted notion that CREB is a primary hub of activity-dependent gene expression regulation. Furthermore, this study uncovers unexpected posttranscriptional and posttranslational gene expression regulatory mechanisms involving differential promoter/exon usage and miRNA-mediated modulation of gene expression. Finally, exploratory experiments suggest that constitutive activation of the CREB, SRF, EGR1, and FOS regulons impacts various aspects of neuronal functioning, including neuronal survival, neuroprotection and excitability, among others. Overall, our study constitutes the first attempt to directly compare the neuronal regulons of different TFs, providing a comprehensive view of the intricate genetic programs elicited by neuronal activity and laying the foundation for a better understanding of transcriptional networks involved in activity-dependent gene expression.