Upon experience, humans can learn, acquire new skills and adapt to their environment. This is explained by the exceptional plasticity of the brain. When neurons receive a message, they trigger cellular programs aiming to modify their structure and functioning. These cellular modifications represent the physical support of learning. Understanding which molecular mechanisms that allow this cellular plasticity is a major challenge. Transcription programs induced by neuronal stimulation are crucial for plasticity. However, one poorly appreciated aspect of transcription is its significant temporal constraint. Synthesis of RNAs can require many hours, especially for long genes whose expression is overrepresented in the brain. Therefore, the impact of new transcription is drastically limited in respect to the rapid plastic events that occurs in seconds/minutes range.

I previously discovered a transcription-independent mechanism that rapidly regulates gene expression in response to neuronal stimulation. This mechanism relies on nuclear storage of pre-existing transcripts and their rapid mobilization in response to signals. In primary neurons, we observed that a substantial population of transcripts retains select introns. Intron corresponds to a non-coding part of transcript that needs to be removed by splicing to generate a mature mRNA. At rest, these intron-retaining transcripts are stably maintained in the nucleus. However, upon neuronal stimulation, these RNAs finalize their splicing in few minutes and are subsequently used for protein production.

The discovery of this new mechanism has opened unsuspected tracks in respect to the molecular pathways contributing to learning. The goal of this proposal is to explore to which extent intron retention and excision is deployed in living animals and how it contributes to neuronal plasticity. First, I will use transcriptome-wide methods as well as single-molecule RNA visualization approaches to probe in vivo intron retention profiles and their regulation under physiological stimulation. Second, I will combine a targeted analysis of the public data from the recently updated Encode consortium, and the elaboration of minigene assays to identify the regulatory determinants of intron retention and excision. Ultimately, I will elaborate selective antisense oligonucleotides and apply them in living animals with high-precision surgical procedures to control intron patterns and explore the impact of intron regulation on neuron biology in mouse.