Trans-cellular control of synapse properties by a cell type-specific splicing regulator

The recognition of synaptic partners and specification of synaptic properties are fundamental for the function of neuronal circuits. ‘Terminal selector’ transcription factors coordinate the expression of terminal gene batteries that specify cell type-specific properties. Moreover, pan-neuronal alternative splicing regulators have been implicated in directing neuronal differentiation. However, the cellular logic of how splicing regulators instruct specific synaptic properties remains poorly understood. Here, we combine genome-wide mapping of mRNA targets and cell type-specific loss-of-function studies to uncover the contribution of the nuclear RNA binding protein SLM2 to hippocampal synapse specification. Focusing on hippocampal pyramidal cells and SST-positive GABAergic interneurons, we find that SLM2 preferentially binds and regulates alternative splicing of transcripts encoding synaptic proteins, thereby generating cell type-specific isoforms. In the absence of SLM2, cell type-specification, differentiation, and viability are unaltered and neuronal populations exhibit normal intrinsic properties. By contrast, cell type-specific loss of SLM2 results in highly selective, non-cell autonomous synaptic phenotypes, altered synaptic transmission, and associated defects in a hippocampus-dependent memory task. Thus, alternative splicing provides a critical layer of gene regulation that instructs specification of neuronal connectivity in a trans-synaptic manner

A cell-type-specific alternative splicing regulator shapes synapse properties in a trans-synaptic manner

The specification of synaptic properties is fundamental for the function of neuronal circuits. "Terminal selector" transcription factors coordinate terminal gene batteries that specify cell-type-specific properties. Moreover, pan-neuronal splicing regulators have been implicated in directing neuronal differentiation. However, the cellular logic of how splicing regulators instruct specific synaptic properties remains poorly understood. Here, we combine genome-wide mapping of mRNA targets and cell-type-specific loss-of-function studies to uncover the contribution of the RNA-binding protein SLM2 to hippocampal synapse specification. Focusing on pyramidal cells and somatostatin (SST)-positive GABAergic interneurons, we find that SLM2 preferentially binds and regulates alternative splicing of transcripts encoding synaptic proteins. In the absence of SLM2, neuronal populations exhibit normal intrinsic properties, but there are non-cell-autonomous synaptic phenotypes and associated defects in a hippocampus-dependent memory task. Thus, alternative splicing provides a critical layer of gene regulation that instructs specification of neuronal connectivity in a trans-synaptic manner

Optimizing Nervous System-Specific Gene Targeting with Cre Driver Lines: Prevalence of Germline Recombination and Influencing Factors.

The Cre-loxP system is invaluable for spatial and temporal control of gene knockout, knockin, and reporter expression in the mouse nervous system. However, we report varying probabilities of unexpected germline recombination in distinct Cre driver lines designed for nervous system-specific recombination. Selective maternal or paternal germline recombination is showcased with sample Cre lines. Collated data reveal germline recombination in over half of 64 commonly used Cre driver lines, in most cases with a parental sex bias related to Cre expression in sperm or oocytes. Slight differences among Cre driver lines utilizing common transcriptional control elements affect germline recombination rates. Specific target loci demonstrated differential recombination; thus, reporters are not reliable proxies for another locus of interest. Similar principles apply to other recombinase systems and other genetically targeted organisms. We hereby draw attention to the prevalence of germline recombination and provide guidelines to inform future research for the neuroscience and broader molecular genetics communities

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

RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse in brain and difficult to accurately identify and quantify. We developed a new approach to address this challenge, combining long-range PCR and nanopore sequencing with a novel bioinformatics pipeline. We identify the full-length coding transcripts of CACNA1C in human brain. CACNA1C is a psychiatric risk gene that encodes the voltage-gated calcium channel CaV1.2. We show that CACNA1C’s transcript profile is substantially more complex than appreciated, identifying 38 novel exons and 241 novel transcripts. Importantly, many of the novel variants are abundant, and predicted to encode channels with altered function. The splicing profile varies between brain regions, especially in cerebellum. We demonstrate that human transcript diversity (and thereby protein isoform diversity) remains under-characterised, and provide a feasible and cost-effective methodology to address this. A detailed understanding of isoform diversity will be essential for the translation of psychiatric genomic findings into pathophysiological insights and novel psychopharmacological targets

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.

Synaptic Ménage à Trois

Regulation of neurotransmitter receptor localization is critical for synaptic function and plasticity. In this issue of Neuron, Matsuda and colleagues (Matsuda et al., 2016) uncover a transsynaptic complex consisting of neurexin-3, C1q-like proteins, and kainate receptors that drives glutamate receptor clustering at hippocampal synapses

Regulation of Neuronal Differentiation, Function, and Plasticity by Alternative Splicing

Posttranscriptional mechanisms provide powerful means to expand the coding power of genomes. In nervous systems, alternative splicing has emerged as a fundamental mechanism not only for the diversification of protein isoforms but also for the spatiotemporal control of transcripts. Thus, alternative splicing programs play instructive roles in the development of neuronal cell type-specific properties, neuronal growth, self-recognition, synapse specification, and neuronal network function. Here we discuss the most recent genome-wide efforts on mapping RNA codes and RNA-binding proteins for neuronal alternative splicing regulation. We illustrate how alternative splicing shapes key steps of neuronal development, neuronal maturation, and synaptic properties. Finally, we highlight efforts to dissect the spatiotemporal dynamics of alternative splicing and their potential contribution to neuronal plasticity and the mature nervous system. Expected final online publication date for the Annual Review of Cell and Developmental Biology Volume 34 is October 6, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates

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

Nervous system function relies on complex assemblies of distinct neuronal cell types that have 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 via alternative splicing is a central mechanism for the functional specification of neuronal cell types and circuits

Association between thyroid hormones and TRAIL

11noRecent studies suggest that a circulating protein called TRAIL (TNF-related apoptosis-inducing ligand) might have a role in the regulation of body weight and metabolism. Interestingly, thyroid hormones seem to increase TRAIL tissue expression. This study aimed at evaluating whether overt thyroid disorders affected circulating TRAIL levels.openopenBernardi, Stella; Bossi, Fleur; Toffoli, Barbara; Giudici, Fabiola; Bramante, Alessandra; Furlanis, Giulia; Stenner, Elisabetta; Secchiero, Paola; Zauli, Giorgio; Carretta, Renzo; Fabris, BrunoBernardi, Stella; Bossi, Fleur; Toffoli, Barbara; Giudici, Fabiola; Bramante, Alessandra; Furlanis, Giulia; Stenner, Elisabetta; Secchiero, Paola; Zauli, Giorgio; Carretta, Renzo; Fabris, Brun