Transcriptional Mechanisms Underlying Neuronal Activity-Dependent Plasticity

Impairment in learning and memory is a well-established cognitive symptom that is manifested in many psychiatric diseases including autism and schizophrenia. Studies have shown that long-lasting memory formation is mediated by rapid changes in nuclear gene expression in response to learning-induced sensory experience. Despite these findings, there is a significant gap in our knowledge as to how sensory information is precisely translated into specific transcriptional outputs. Recently, a class of long noncoding RNAs that are transcribed bidirectionally from the enhancers of activity-dependent genes in neurons (eRNAs) has been identified. My first project studied the function of eRNAs of two immediate early genes Activity-regulated cytoskeletal protein (Arc) and Growth arrest and DNA-damage-inducible, beta (Gadd45b), which have been implicated in mediating synaptic plasticity. Using a knockdown approach, we found that eRNAs are necessary for the full induction of their target genes in response to membrane depolarization. eRNAs specifically regulate the early elongation stage of transcription by allowing for efficient release of paused RNA polymerase II (RNAPII) from the promoters of activity-regulated genes. Knockdown of eRNAs results in the retention of an RNAPII pausing factor, Negative Elongation Factor (NELF), at the target gene promoter. eRNAs directly bind to NELF during stimulated conditions, suggesting that eRNAs interact with NELF to facilitate its release from the promoter, thus resulting in efficient and precisely timed gene activation. These data define a new role for the spatiotemporally controlled expression of regulatory RNAs in the experience-dependent gene expression network. My second project aimed to identify the transcriptional program activated when activity levels are suppressed. Homeostatic scaling allows neurons to maintain stable activity patterns by globally altering their synaptic strength in response to changing activity levels. Decreasing activity leads to an upregulation in synaptic strength, as seen by increases in AMPA mediated mEPSCs. It was previously shown that the increase in mEPSC amplitude could be blocked by a transcription inhibitor, suggesting that transcription is necessary for the scaling response. However, little is known about the genes directly regulated by activity suppression or the signaling mechanisms underlying the transcriptional control. Using RNA-Seq, we identified nearly 100 genes that were specifically upregulated in response to activity suppression. Neuronal pentraxin-1 (Nptx1), previously shown to promote AMPAR clustering, was increased ~3 fold, and knockdown of this gene blocked the increase in mEPSC amplitudes. SRF is a key transcription factor in regulating Nptx1 induction, which is calcium-dependent, indicating the existence of an active pathway to control transcription. Taken together, this study defines a novel transcriptional program that is able to sense the absence of activity and coordinate the global increase in synaptic strength.