Alternative splice codes for neuronal diversification and synapse specification

Mammalian nervous systems exhibit an immense structural and functional complexity ranging from billions of neurons to their precise synaptic communication. Neuronal circuits consist of hierarchical assemblies of highly specialized neuronal cell types. Their intrinsic properties and the functional specification of their synapses are fundamental for how circuits process information. However, how diverse classes of neurons establish their cellular and synaptic specificity remains largely unclear. In this thesis, I explored whether cell type-specific alternative splicing programs contribute to the regulation of neuronal and synaptic properties, thereby shaping neuronal connectivity and circuit function.
To investigate whether alternative splicing programs play cell type-specific roles in the mouse brain, I performed global assessments of alternative splicing regulation across neuronal cell classes as well as targeted loss of function studies for one specific alternative splicing regulator. I focused on the RNA binding protein SLM2 which exhibits a remarkable neuronal cell class-specific expression in the mouse brain and had been previously implicated in the regulation of alternative splicing of the synaptic adhesion molecules Neurexin1,2, and 3 (Ehrmann et al., 2013; Iijima et al., 2011). Surprisingly, we found that SLM2 regulates only a handful of transcripts and that loss of SLM2 results in highly selective alterations at glutamatergic synapses in the mouse hippocampus. Genetic correction of the SLM2-dependent target exon of Neurexin 1 was sufficient to rescue synaptic deficits and alterations in the behavior of the Slm2 knock-out animals. Thus, the SLM2 alternative splicing program is highly dedicated to control synapse specification and function in the hippocampus.
In a complementary effort, I investigated how alternative splicing programs are arrayed across different neuronal populations of the forebrain. Systematic mapping of ribosome-associated transcript isoforms in genetically defined cell populations of wild-type animals uncovered extensive transcript isoform diversity across neuronal classes. This revealed that the important drivers for diversification in glutamatergic and GABAergic cells are alternative splicing and transcription start sites. Importantly, we uncovered that such cell class-specific alternative splicing programs mainly target genes implicated in regulating synaptic functions and the intrinsic properties of neurons.
Finally, I explored whether a single RNA binding protein controls common or divergent splicing events and cellular functions in different neuronal populations. We analyzed SLM2-dependent alternative splicing programs in two hippocampal glutamatergic cell classes and somatostatin positive GABAergic neurons. Our findings indicate that there are unique sets of SLM2-dependent transcript isoforms and divergent synaptic phenotypes in different cell populations.
In sum, this work uncovers major roles for cell class-specific alternative splicing programs in the genetic determination of neuronal function and synapse specification