Prevalent presence of periodic actin–spectrin-based membrane skeleton in a broad range of neuronal cell types and animal species

Actin, spectrin, and associated molecules form a periodic, submembrane cytoskeleton in the axons of neurons. For a better understanding of this membrane-associated periodic skeleton (MPS), it is important to address how prevalent this structure is in different neuronal types, different subcellular compartments, and across different animal species. Here, we investigated the organization of spectrin in a variety of neuronal- and glial-cell types. We observed the presence of MPS in all of the tested neuronal types cultured from mouse central and peripheral nervous systems, including excitatory and inhibitory neurons from several brain regions, as well as sensory and motor neurons. Quantitative analyses show that MPS is preferentially formed in axons in all neuronal types tested here: Spectrin shows a long-range, periodic distribution throughout all axons but appears periodic only in a small fraction of dendrites, typically in the form of isolated patches in subregions of these dendrites. As in dendrites, we also observed patches of periodic spectrin structures in a small fraction of glial-cell processes in four types of glial cells cultured from rodent tissues. Interestingly, despite its strong presence in the axonal shaft, MPS is disrupted in most presynaptic boutons but is present in an appreciable fraction of dendritic spine necks, including some projecting from dendrites where such a periodic structure is not observed in the shaft. Finally, we found that spectrin is capable of adopting a similar periodic organization in neurons of a variety of animal species, including Caenorhabditis elegans, Drosophila, Gallus gallus, Mus musculus, and Homo sapiens.

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Prevalent Presence of Periodic Actin-spectrin-based Membrane Skeleton in a Broad Range of Neuronal Cell Types and Animal Species

10.1101/045856 ◽

2016 ◽

Cited By ~ 1

Author(s):

Jiang He ◽

Ruobo Zhou ◽

Zhuhao Wu ◽

Monica Carrasco ◽

Peri Kurshan ◽

...

Keyword(s):

Glial Cell ◽

Animal Species ◽

Homo Sapiens ◽

Neuronal Cell ◽

Cell Types ◽

Membrane Skeleton ◽

Brain Regions ◽

Inhibitory Neurons ◽

Periodic Distribution ◽

Neuronal Types

AbstractActin, spectrin and associated molecules form a periodic, sub-membrane cytoskeleton in the axons of neurons. For a better understanding of this membrane-associated periodic skeleton (MPS), it is important to address how prevalent this structure is in different neuronal types, different subcellular compartments, and across different animal species. Here, we investigated the organization of spectrin in a variety of neuronal and glial-cell types. We observed the presence of MPS in all of the tested neuronal types cultured from mouse central and peripheral nervous systems, including excitatory and inhibitory neurons from several brain regions, as well as sensory and motor neurons. Quantitative analyses show that MPS is preferentially formed in axons in all neuronal types tested here: spectrin shows a long-range, periodic distribution throughout all axons, but only appears periodic in a small fraction of dendrites, typically in the form of isolated patches in sub-regions of these dendrites. As in dendrites, we also observed patches of periodic spectrin structures in a small fraction of glial-cell processes in four types of glial cells cultured from rodent tissues. Interestingly, despite its strong presence in the axonal shaft, MPS is absent in most presynaptic boutons, but is present in a substantial fraction of dendritic spine necks, including some projecting from dendrites where such a periodic structure is not observed in the shaft. Finally, we found that spectrin is capable of adopting a similar periodic organization in neurons of a variety of animal species, including Caenorhabditis elegans, Drosophila, Gallus gallus, Mus musculus and Homo sapiens.

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Single-nuclei transcriptomics of schizophrenia prefrontal cortex primarily implicates neuronal subtypes

10.1101/2020.07.29.227355 ◽

2020 ◽

Author(s):

Benjamin C. Reiner ◽

Richard C. Crist ◽

Lauren M. Stein ◽

Andrew E. Weller ◽

Glenn A. Doyle ◽

...

Keyword(s):

Prefrontal Cortex ◽

Differentially Expressed Genes ◽

Neuronal Cell ◽

Cell Types ◽

Brain Regions ◽

Differentially Expressed ◽

Inhibitory Neurons ◽

Specific Cell ◽

Dorsolateral Prefrontal ◽

Layer V

AbstractTranscriptomic studies of bulk neural tissue homogenates from persons with schizophrenia and controls have identified differentially expressed genes in multiple brain regions. However, the heterogeneous nature prevents identification of relevant cell types. This study analyzed single-nuclei transcriptomics of ∼311,000 nuclei from frozen human postmortem dorsolateral prefrontal cortex samples from individuals with schizophrenia (n = 14) and controls (n = 16). 2,846 differential expression events were identified in 2,195 unique genes in 19 of 24 transcriptomically-distinct cell populations. ∼97% of differentially expressed genes occurred in five neuronal cell types, with ∼63% occurring in a subtype of PVALB+ inhibitory neurons and HTR2C+ layer V excitatory neurons. Differentially expressed genes were enriched for genes localized to schizophrenia GWAS loci. Cluster-specific changes in canonical pathways, upstream regulators and causal networks were identified. These results expand our knowledge of disrupted gene expression in specific cell types and permit new insight into the pathophysiology of schizophrenia.

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GABAergic Neuron Specification in the Spinal Cord, the Cerebellum, and the Cochlear Nucleus

Neural Plasticity ◽

10.1155/2012/921732 ◽

2012 ◽

Vol 2012 ◽

pp. 1-11 ◽

Cited By ~ 13

Author(s):

Kei Hori ◽

Mikio Hoshino

Keyword(s):

Spinal Cord ◽

Nervous System ◽

Cochlear Nucleus ◽

Neuronal Cell ◽

Cell Types ◽

Brain Regions ◽

Lineage Tracing ◽

Inhibitory Neurons ◽

Genetic Lineage ◽

Genetic Lineage Tracing

In the nervous system, there are a wide variety of neuronal cell types that have morphologically, physiologically, and histochemically different characteristics. These various types of neurons can be classified into two groups: excitatory and inhibitory neurons. The elaborate balance of the activities of the two types is very important to elicit higher brain function, because its imbalance may cause neurological disorders, such as epilepsy and hyperalgesia. In the central nervous system, inhibitory neurons are mainly represented by GABAergic ones with some exceptions such as glycinergic. Although the machinery to specify GABAergic neurons was first studied in the telencephalon, identification of key molecules, such as pancreatic transcription factor 1a (Ptf1a), as well as recently developed genetic lineage-tracing methods led to the better understanding of GABAergic specification in other brain regions, such as the spinal cord, the cerebellum, and the cochlear nucleus.

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Extensive Involvement of Alternative Polyadenylation in Single-Nucleus Neurons

Genes ◽

10.3390/genes11060709 ◽

2020 ◽

Vol 11 (6) ◽

pp. 709

Author(s):

Ying Wang ◽

Weixing Feng ◽

Siwen Xu ◽

Bo He

Keyword(s):

Rna Binding ◽

Neuronal Cell ◽

Alternative Polyadenylation ◽

Cell Types ◽

Inhibitory Neurons ◽

Cell Populations ◽

Motif Analysis ◽

Eukaryotic Genes ◽

Single Nucleus ◽

Extensive Involvement

Cleavage and polyadenylation are essential processes that can impact many aspects of mRNA fate. Most eukaryotic genes have alternative polyadenylation (APA) events. While the heterogeneity of mRNA polyadenylation isoform choice has been studied in specific tissues, less attention has been paid to the neuronal heterogeneity of APA selection at single-nucleus resolution. APA is highly controlled during development and neuronal activation, however, to what extent APA events vary in a specific neuronal cell population and the regulatory mechanisms are still unclear. In this paper, we investigated dynamic APA usage in different cell types using snRNA-seq data of 1424 human brain cells generated by single-cell 3′ RNA sequencing. We found that distal APA sites are not only favored by global neuronal cells, but that their usage also varies between the principal types of neuronal cell populations (excitatory neurons and inhibitory neurons). A motif analysis and a gene functional analysis indicated the enrichment of RNA-binding protein (RBP) binding sites and neuronal functions for the set of genes with neuron-enhanced distal PAS usage. Our results revealed the extensive involvement of APA regulation in neuronal populations at the single-nucleus level, providing new insights into roles for APA in specific neuronal cell populations, as well as utility in future functional studies.

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Optogenetic Technology and Its In Vivo Applications

Einstein Journal of Biology and Medicine ◽

10.23861/ejbm20112776 ◽

2016 ◽

Vol 27 (2) ◽

pp. 78

Author(s):

Simon Gelman

Keyword(s):

Cell Biology ◽

Nonhuman Primates ◽

Animal Species ◽

Neural Circuits ◽

Neuronal Cell ◽

Cell Types ◽

Whole Cells ◽

Neuronal Populations ◽

Novel Technology

Optogenetics is a novel technology with the widely acknowledged potential to revolutionize cell biology and neuroscience. Essentially, optogenetic methods integrate optical and genetic tools to control the activity of whole cells or subcellular events. In recent years, optogenetics has been used to activate and to inhibit genetically defined neuronal populations within neural circuits. As such, it has been used to show the sufficiency or the necessity of specific neuronal cell types in generating behaviors across a number of animal species. When employed in rodent models of human neurological and psychiatric disorders, optogenetics has provided clinically relevant insights into the function of pathologic neural circuits. Recent progress in the in vivo applications of this methodology is reviewed in this article, with particular focus on behavioral applications in nematodes, fish, rodents, and nonhuman primates.

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Simultaneous pathway engagement of translation in astrocytes, circadian rhythm in GABAergic neurons and cytoskeleton in glutamatergic neurons precede electroencephalographic changes in neurodegenerative prion disease

10.1101/2021.11.26.470101 ◽

2021 ◽

Author(s):

Lech Tadeusz Kaczmarczyk ◽

Melvin Schleif ◽

Lars Dittrich ◽

Rhiannan Williams ◽

Marusa Koderman ◽

...

Keyword(s):

Circadian Rhythm ◽

Prion Disease ◽

Disease Onset ◽

Disease Process ◽

Cell Types ◽

Brain Regions ◽

Inhibitory Neurons ◽

Clinical Feature ◽

Outward Appearance ◽

Theta Power

Selective vulnerability is an enigmatic feature of neurodegenerative diseases (NDs), whereby a widely expressed protein causes lesions in specific brain regions and cell types. This selectivity may arise from cells possessing varying capacities to regain proteostasis when stressed by cytotoxic protein conformers. Using the RiboTag method in mice, translational responses of five neural subtypes to acquired prion disease (PrD) were measured. Pre-onset and disease onset timepoints were chosen based on longitudinal electroencephalography (EEG) that revealed a gradual increase in theta power between 10- and 18-weeks after prion injection, resembling a clinical feature of human PrD. At disease onset, marked by significantly increased theta power and histopathological lesions, mice had pronounced translatome changes in all five cell types despite having a normal outward appearance. Remarkably, at a pre-onset stage, prior to EEG and neuropathological changes, we found that 1) translatomes of astrocytes indicated a sharply reduced synthesis of ribosomal and mitochondrial components, 2) excitatory neurons showed increased expression of cytoskeletal genes, and 3) inhibitory neurons revealed reduced expression of circadian rhythm network genes. Further assessment for the role of circadian rhythms using a jet lag paradigm modestly exacerbated disease. These data demonstrate that early translatome responses to neurodegeneration emerge prior to other signs of disease and are unique to different cell types. Therapeutic strategies may need to target multiple pathways, each in specific populations of cells, early in the disease process.

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FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory

eLife ◽

10.7554/elife.46919 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 16

Author(s):

Kirsty Sawicka ◽

Caryn R Hale ◽

Christopher Y Park ◽

John J Fak ◽

Jodi E Gresack ◽

...

Keyword(s):

Pyramidal Neurons ◽

Rna Binding ◽

Fragile X ◽

Neuronal Cell ◽

Cell Types ◽

Brain Regions ◽

Cell Type ◽

Ca1 Pyramidal Neurons ◽

Mrna Targets ◽

Specific Regulation

Loss of the RNA binding protein FMRP causes Fragile X Syndrome (FXS), the most common cause of inherited intellectual disability, yet it is unknown how FMRP function varies across brain regions and cell types and how this contributes to disease pathophysiology. Here we use conditional tagging of FMRP and CLIP (FMRP cTag CLIP) to examine FMRP mRNA targets in hippocampal CA1 pyramidal neurons, a critical cell type for learning and memory relevant to FXS phenotypes. Integrating these data with analysis of ribosome-bound transcripts in these neurons revealed CA1-enriched binding of autism-relevant mRNAs, and CA1-specific regulation of transcripts encoding circadian proteins. This contrasted with different targets in cerebellar granule neurons, and was consistent with circadian defects in hippocampus-dependent memory in Fmr1 knockout mice. These findings demonstrate differential FMRP-dependent regulation of mRNAs across neuronal cell types that may contribute to phenotypes such as memory defects and sleep disturbance associated with FXS.

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An atlas of gene regulatory elements in adult mouse cerebrum

Nature ◽

10.1038/s41586-021-03604-1 ◽

2021 ◽

Vol 598 (7879) ◽

pp. 129-136

Author(s):

Yang Eric Li ◽

Sebastian Preissl ◽

Xiaomeng Hou ◽

Ziyang Zhang ◽

Kai Zhang ◽

...

Keyword(s):

Glial Cell ◽

Target Genes ◽

Adult Mouse ◽

Cell Types ◽

Regulatory Elements ◽

Inhibitory Neurons ◽

Mammalian Brain ◽

Regulatory Sequences ◽

Subcortical Structures ◽

Gene Regulatory

AbstractThe mammalian cerebrum performs high-level sensory perception, motor control and cognitive functions through highly specialized cortical and subcortical structures1. Recent surveys of mouse and human brains with single-cell transcriptomics2–6 and high-throughput imaging technologies7,8 have uncovered hundreds of neural cell types distributed in different brain regions, but the transcriptional regulatory programs that are responsible for the unique identity and function of each cell type remain unknown. Here we probe the accessible chromatin in more than 800,000 individual nuclei from 45 regions that span the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to map the state of 491,818 candidate cis-regulatory DNA elements in 160 distinct cell types. We find high specificity of spatial distribution for not only excitatory neurons, but also most classes of inhibitory neurons and a subset of glial cell types. We characterize the gene regulatory sequences associated with the regional specificity within these cell types. We further link a considerable fraction of the cis-regulatory elements to putative target genes expressed in diverse cerebral cell types and predict transcriptional regulators that are involved in a broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Our results provide a foundation for comprehensive analysis of gene regulatory programs of the mammalian brain and assist in the interpretation of noncoding risk variants associated with various neurological diseases and traits in humans.

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Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing

10.1101/2021.01.27.428525 ◽

2021 ◽

Author(s):

Huijuan Feng ◽

Daniel F. Moakley ◽

Shuonan Chen ◽

Melissa G. McKenzie ◽

Vilas Menon ◽

...

Keyword(s):

Alternative Splicing ◽

Rna Binding ◽

Rna Binding Proteins ◽

Neuronal Cell ◽

Cell Types ◽

Mammalian Brain ◽

Differential Splicing ◽

Hierarchical Levels ◽

Neuronal Types ◽

And Function

AbstractThe enormous neuronal cellular diversity in the mammalian brain, which is highly prototypical and organized in a hierarchical manner, is dictated by cell type-specific gene regulatory programs at the molecular level. Although prevalent in the brain, contribution of alternative splicing (AS) to the molecular diversity across neuronal cell types is just starting to emerge. Here we systematically investigated AS regulation across over 100 transcriptomically defined neuronal types of the adult mouse cortex using deep single cell RNA-sequencing (scRNA-seq) data. We found distinct splicing programs between glutamatergic and GABAergic neurons and between subclasses within each neuronal class, consisting of overlapping sets of alternative exons showing differential splicing at multiple hierarchical levels. Using an integrative approach, our analysis suggests that RNA-binding proteins (RBPs) Celf1/2, Mbnl2 and Khdrbs3 are preferentially expressed and more active in glutamatergic neurons, while Elavl2 and Qk are preferentially expressed and more active in GABAergic neurons. Importantly, these and additional RBPs also contribute to differential splicing between neuronal subclasses at multiple hierarchical levels, and some RBPs drive splicing dynamics that do not conform to the hierarchical structure defined by the transcriptional profiles. Thus, our results suggest graded regulation of AS across neuronal cell types, which provides a molecular mechanism orthogonal to, rather than downstream of, transcriptional regulation in specifying neuronal identity and function.SignificanceAlternative splicing (AS) is extensively used in the mammalian brain, but its contribution to the molecular and cellular diversity across neuronal cell types remains poorly understood. Through systematic and integrative analysis of AS regulation across over 100 transcriptomically defined cortical neuronal types, we found neuronal subclass-specific splicing regulatory programs consists of overlapping alternative exons showing differential splicing at multiple hierarchical levels. This graded AS regulation is controlled by unique combinations of RNA-binding proteins (RBPs). Importantly, these RBPs also drive splicing dynamics across neuronal cell types that do not conform to the hierarchical taxonomy established based on transcriptional profiles, suggesting that the graded AS regulation provides a molecular mechanism orthogonal to transcriptional regulation in specifying neuronal identity and function.

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Extracellular Interactions of Alpha-Synuclein in Multiple System Atrophy

International Journal of Molecular Sciences ◽

10.3390/ijms19124129 ◽

2018 ◽

Vol 19 (12) ◽

pp. 4129 ◽

Cited By ~ 6

Author(s):

Dario Valdinocci ◽

Rowan Radford ◽

Michael Goulding ◽

Junna Hayashi ◽

Roger Chung ◽

...

Keyword(s):

Multiple System Atrophy ◽

Disease Process ◽

Neuronal Cell ◽

Cell Loss ◽

Cell Types ◽

Brain Regions ◽

Alpha Synuclein ◽

Current Evidence ◽

Extracellular Milieu ◽

The Brain

Multiple system atrophy, characterized by atypical Parkinsonism, results from central nervous system (CNS) cell loss and dysfunction linked to aggregates of the normally pre-synaptic α-synuclein protein. Mostly cytoplasmic pathological α-synuclein inclusion bodies occur predominantly in oligodendrocytes in affected brain regions and there is evidence that α-synuclein released by neurons is taken up preferentially by oligodendrocytes. However, extracellular α-synuclein has also been shown to interact with other neural cell types, including astrocytes and microglia, as well as extracellular factors, mediating neuroinflammation, cell-to-cell spread and other aspects of pathogenesis. Here, we review the current evidence for how α-synuclein present in the extracellular milieu may act at the cell surface to drive components of disease progression. A more detailed understanding of the important extracellular interactions of α-synuclein with neuronal and non-neuronal cell types both in the brain and periphery may provide new therapeutic targets to modulate the disease process.

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