Beyond gene expression: post-transcriptional mechanisms for the regulation of neuronal identity and function

Brain function relies on complex assemblies of multiple types of excitatory and inhibitory neurons: while the first are responsible for the efficient input processing and transmission, the latter temporally and spatially modulate this flow of information. Each of these neuron types are characterized by distinctive structural, physiological and molecular features, but how this diversity is established during development and maintained throughout adulthood remains one of the most fascinating biomedical problems. Recent studies highlighted how the embryonic differentiation of precursors into specific neuron types is accompanied by finely controlled gene expression signatures. However, the molecular mechanisms that specify properties of mature neurons remain largely unknown.
Neurons exhibit an especially large extent of transcript diversification and regulation by several post-transcriptional mechanisms. In the present work, I investigated whether modulation of RNA processing and metabolism in neurons can define distinct cell types and their unique anatomical and functional properties.
Firstly, in a complementary effort, I performed genetic ribosome tagging in distinct excitatory and inhibitory neuron populations of the mouse brain and performed an extensive genome-wide mapping of ribosome-associated mRNAs. For the first time we identified hundreds of differentially expressed alternative transcripts generated by alternative splicing (AS) and transcription start site usage (ATSS) that can reliably distinguish neuron classes with distinct properties and anatomical localizations in the brain. Interestingly, transcripts that undergo cell type-specific alternative splicing mostly encode proteins critical for synaptic interactions and intrinsic electrical properties of neurons. This demonstrates that AS represents a molecular mechanisms that is particularly tailored to shape and sculpt the characteristic features of functional neurons in a network. Moreover, we further identified differentially expressed RNA-binding proteins that reliably shift splicing patterns of reporters for differentially regulated transcripts. These splicing regulators represent candidates for future in vivo studies on the modulation of respective splicing events.
In a second project, I explored the functional impact of the cell type-selective expression of the RNA-binding protein Rbms3 in GABAergic neurons. In particular, I investigated the molecular mechanism used by Rbms3 to regulate target mRNAs’ metabolism in the cytoplasm of this cell class. Moreover, I showed that genetic ablation of Rbms3 results in both transcriptomic and proteomic defects in the mouse neocortex, which revealed an increase in cellular stress upon Rbms3 loss. Finally, Rbms3 loss-of-function in GABAergic neurons resulted in increased anxiety-related behaviors in mice, suggesting a fundamental role of this RNA-binding protein in modulating the correct functioning of interneurons in the mouse brain.