Landscape of ribosome-engaged transcript isoforms reveals extensive neuronal-cell-class-specific alternative splicing programs

Abstract

Nervous system function relies on complex assemblies of distinct neuronal cell types with unique anatomical and functional properties instructed by molecular programs. Alternative splicing is a key mechanism for the expansion of molecular repertoires and protein splice isoforms shape neuronal cell surface recognition and function. However, the logic of how alternative splicing programs are arrayed across neuronal cells types is poorly understood. We systematically mapped ribosome-associated transcript isoforms in genetically-defined neuron types of the mouse forebrain. Our dataset provides an extensive resource of transcript diversity across major neuron classes. We find that neuronal transcript isoform profiles reliably distinguish even closely-related classes of pyramidal cells and inhibitory interneurons in the mouse hippocampus and neocortex. These highly specific alternative splicing programs selectively control synaptic proteins and intrinsic neuronal properties. Thus, transcript diversification by alternative splicing is a central mechanism for the functional specification of neuronal cell types and circuits.Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:

Co-expression networks uncover regulation of splicing and transcription markers of disease

“…An interesting finding from the gene-isoform Graphical Lasso analysis is the enrichment of the Ribosome (KEGG mmu03010), structural constituent of ribosome (GO:0003735), structural molecule activity (GO:0005198) and RNA binding (GO:0003723) categories among the Gene-Isoform hubs in both regions associated with response to pain and to reward stimuli. That is in agreement with the reports that the ribosome and RNA binding is engaged in alternative splicing events [25][26][27]. Also, the enriched categories such as Glutamatergic synapse, GABAergic synapse and Retrograde endocannabinoid signaling are consistent with reports of the association of these pathways and neuropathic pain [11,28].…”

Ribosomal profiling during prion disease uncovers progressive translational derangement in glia but not in neurons

“…We next identified genes that were differentially translated between the different cell types using Several studies have previously assessed ribosome-associated RNAs in the same cell types (Boisvert et al, 2018;Furlanis et al, 2019;Haimon et al, 2018). Using the RiboTag (RT) mouse, which expresses HA-tagged ribosomes in a Cre-dependent manner the authors sequenced the immunoprecipitated RNA directly.…”

“…Alternatively, cell-type specific profiles can be generated from mice expressing tagged ribosomes in the cell type of interest via translating ribosome affinity purification (TRAP) followed by RNA sequencing (Heiman et al, 2014). RiboTag (RT) mice expressing HA tagged ribosomes in a Cre recombinase dependent manner (Sanz et al, 2009), have been used to profile multiple CNS cell populations without tissue manipulation procedures (Boisvert et al, 2018;Furlanis et al, 2019;Haimon et al, 2018). The datasets generated from these experiments are likely to reflect the endogenous expression of mRNA very closely.…”

Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain

“…Most of these SNPs are non-coding [2][3][4] , implying that they mediate disease associations by influencing aspects of RNA expression. Of the various mechanisms of RNA regulation, the possibility that psychiatric risk SNPs might influence RNA splicing is particularly appealing, given its exquisite, cell type-specific regulation and its key role in determining neuronal properties 5 . Consistent with this hypothesis, at a global level, cellular studies emphasise RNA splicing as a key mechanism mediating the effect of disease-associated, non-coding variants in complex disorders, including schizophrenia 6 .…”