scholarly journals Timing and Duration of Gbx2 Expression Delineates Thalamocortical and Dopaminergic Medial Forebrain Bundle Circuitry

2019 ◽  
Author(s):  
Elizabeth Normand ◽  
Catherine Browning ◽  
Mark Zervas
Keyword(s):  
Gene Expression ◽  
Medial Forebrain Bundle ◽  
Neural Circuit ◽  
Temporal Dynamics ◽  
Neuronal Cell ◽  
Cell Types ◽  
Dopamine Neurons ◽  
Genetic Lineage ◽  
Thalamocortical Axons ◽  
Circuit Development

SUMMARYGene expression is a dynamic process, which is highly coordinated during development to ensure the proper allocation and identity of neuronal cell types within the brain. Equally important during neurodevelopment is how cohorts of neurons establish axonal projections that innervate terminal target sites. We sought to bridge the temporal dynamics of gene expression, within a specific genetic lineage, to the establishment of neuronal circuits derived from cohorts of the lineage-specific progenitors. A central goal was to be able to accomplish genetic inducible circuit mapping non-invasively and with commonly available CreER/loxP technology. Specifically, we genetically marked thalamic neuron progenitors that expressed the transcription factor Gbx2 at an early embryonic stage and tracked the formation of lineage-derived thalamocortical axons during embryogenesis. We then assessed the neural circuitry at an early postnatal stage. We show that the temporal specificity of lineage marking provides a high degree of clarity for following neural circuit development. We also determined that the onset and duration of gene expression can delineate subsets of neural circuits derived from a common lineage. For example, we uncovered a novel contribution of Gbx2-expressing progenitors to midbrain dopamine neurons and dopaminergic axons of the medial forebrain bundle. We anticipate that this system can be instructive in elucidating changes in neural circuit development in both normal development and in mutant mice in which neural circuit formation is altered.

scholarly journals The marked diversity of unique cortical enhancers enables neuron-specific tools by Enhancer-Driven Gene Expression

2018 ◽  
Author(s):  
Stefan Blankvoort ◽  
Menno P. Witter ◽  
James Noonan ◽  
Justin Cotney ◽  
Cliff Kentros
Keyword(s):  
Gene Expression ◽  
Neural Circuit ◽  
Neuronal Cell ◽  
Cell Types ◽  
Regulatory Elements ◽  
List Type ◽  
Enhancer Activity ◽  
Genetic Tools ◽  
Transgenic Lines ◽  
Genetic Mechanisms

SUMMARYUnderstanding neural circuit function requires individually addressing their component parts: specific neuronal cell types. However, not only do the precise genetic mechanisms specifying neuronal cell types remain obscure, access to these neuronal cell types by transgenic techniques also remains elusive. While most genes are expressed in the brain, the vast majority are expressed in many different kinds of neurons, suggesting that promoters alone are not sufficiently specific to distinguish cell types. However, there are orders of magnitude more distal genetic cis-regulatory elements controlling transcription (i.e. enhancers), so we screened for enhancer activity in microdissected samples of mouse cortical subregions. This identified thousands of novel putative enhancers, many unique to particular cortical subregions. Pronuclear injection of expression constructs containing such region-specific enhancers resulted in transgenic lines driving expression in distinct sets of cells specifically in the targeted cortical subregions, even though the parent gene’s promoter was relatively nonspecific. These data showcase the promise of utilizing the genetic mechanisms underlying the specification of diverse neuronal cell types for the development of genetic tools potentially capable of targeting any neuronal circuit of interest, an approach we call Enhancer-Driven Gene Expression (EDGE).HighlightsEnhancer ChIP-seq of cortical subregions reveals 59372 putative enhancers.3740 of these are specific to particular cortical subregions.This reflects the remarkable anatomical diversity of the adult cortex.Unique enhancers provide a means to make targeted cell-type specific genetic tools.

scholarly journals Single-nucleus RNA sequencing of mouse auditory cortex reveals critical period triggers and brakes

2020 ◽  
Vol 117 (21) ◽  
pp. 11744-11752 ◽  
Author(s):  
Brian T. Kalish ◽  
Tania R. Barkat ◽  
Erin E. Diel ◽  
Elizabeth J. Zhang ◽  
Michael E. Greenberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Auditory Cortex ◽  
Rna Sequencing ◽  
Critical Period ◽  
Neural Circuit ◽  
Developmental Process ◽  
Brain Plasticity ◽  
Cell Types ◽  
Altered Expression ◽  
Single Nucleus

Auditory experience drives neural circuit refinement during windows of heightened brain plasticity, but little is known about the genetic regulation of this developmental process. The primary auditory cortex (A1) of mice exhibits a critical period for thalamocortical connectivity between postnatal days P12 and P15, during which tone exposure alters the tonotopic topography of A1. We hypothesized that a coordinated, multicellular transcriptional program governs this window for patterning of the auditory cortex. To generate a robust multicellular map of gene expression, we performed droplet-based, single-nucleus RNA sequencing (snRNA-seq) of A1 across three developmental time points (P10, P15, and P20) spanning the tonotopic critical period. We also tone-reared mice (7 kHz pips) during the 3-d critical period and collected A1 at P15 and P20. We identified and profiled both neuronal (glutamatergic and GABAergic) and nonneuronal (oligodendrocytes, microglia, astrocytes, and endothelial) cell types. By comparing normal- and tone-reared mice, we found hundreds of genes across cell types showing altered expression as a result of sensory manipulation during the critical period. Functional voltage-sensitive dye imaging confirmed GABA circuit function determines critical period onset, while Nogo receptor signaling is required for its closure. We further uncovered previously unknown effects of developmental tone exposure on trajectories of gene expression in interneurons, as well as candidate genes that might execute tonotopic plasticity. Our single-nucleus transcriptomic resource of developing auditory cortex is thus a powerful discovery platform with which to identify mediators of tonotopic plasticity.

scholarly journals Cellular correlates of cortical thinning throughout the lifespan

2019 ◽  
Author(s):  
D. Vidal-Pineiro ◽  
N. Parker ◽  
J. Shin ◽  
L. French ◽  
H. Grydeland ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Neuronal Cell ◽  
Pyramidal Cells ◽  
Late Life ◽  
Cell Types ◽  
Brain Atlas ◽  
Marker Genes ◽  
Specific Gene ◽  
Cortical Thinning

AbstractCortical thinning occurs throughout the entire life and extends to late-life neurodegeneration, yet the neurobiological substrates are poorly understood. Here, we used a virtual-histology technique and gene expression data from the Allen Human Brain Atlas to compare the regional profiles of longitudinal cortical thinning through life (4004 MRIs) with those of gene expression for several neuronal and non-neuronal cell types. The results were replicated in three independent longitudinal datasets. We found that inter-regional profiles of cortical thinning related to expression profiles for marker genes of CA1 pyramidal cells, astrocytes and microglia during development and in aging. During the two stages of life, the relationships went in opposite directions: greater gene expression related to less thinning in development and vice versa in aging. The association between cortical thinning and cell-specific gene expression was also present in mild cognitive impairment and Alzheimer’s Disease. These findings suggest a role of astrocytes and microglia in promoting and supporting neuronal growth and dendritic structures through life that affects cortical thickness during development, aging, and neurodegeneration. Overall, the findings contribute to our understanding of the neurobiology underlying variations in MRI-derived estimates of cortical thinning through life and late-life disease.

Dendritic trafficking for neuronal growth and plasticity

2013 ◽  
Vol 41 (6) ◽  
pp. 1365-1382 ◽  
Author(s):  
Michael D. Ehlers
Keyword(s):  
Cell Biology ◽  
Neural Circuit ◽  
Cell Communication ◽  
Neuronal Cell ◽  
Cell Types ◽  
The Body ◽  
Plastic Properties ◽  
Electrophysiological Properties ◽  
Differentiated Cells ◽  
Unique Cell

Among the largest cells in the body, neurons possess an immense surface area and intricate geometry that poses many unique cell biological challenges. This morphological complexity is critical for neural circuit formation and enables neurons to compartmentalize cell–cell communication and local intracellular signalling to a degree that surpasses other cell types. The adaptive plastic properties of neurons, synapses and circuits have been classically studied by measurement of electrophysiological properties, ionic conductances and excitability. Over the last 15 years, the field of synaptic and neural electrophysiology has collided with neuronal cell biology to produce a more integrated understanding of how these remarkable highly differentiated cells utilize common eukaryotic cellular machinery to decode, integrate and propagate signals in the nervous system. The present article gives a very brief and personal overview of the organelles and trafficking machinery of neuronal dendrites and their role in dendritic and synaptic plasticity.

scholarly journals Defining developmental diversification of diencephalon neurons through single-cell gene expression profiling

2018 ◽  
Author(s):  
Qiuxia Guo ◽  
James Y. H. Li
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Regulatory Networks ◽  
Neuronal Cell ◽  
Cell Types ◽  
Developmental Trajectory ◽  
Form Complex ◽  
Molecular Features ◽  
Close Relationship ◽  
Cell Groups

ABSTRACTThe embryonic diencephalon gives rise to diverse neuronal cell types, which form complex integration centers and intricate relay stations of the vertebrate forebrain. Prior anecdotal gene expression studies suggest several developmental compartments within the developing diencephalon. In the current study, we utilized single-cell RNA sequencing to profile transcriptomes of dissociated cells from the diencephalon of E12.5 mouse embryos. Through analysis of unbiased transcriptional data, we identified the divergence of different progenitors, intermediate progenitors, and emerging neuronal cell types. After mapping the identified cell groups to their spatial origins, we were able to characterize the molecular features across different cell types and cell states, arising from various diencephalic compartments. Furthermore, we reconstructed the developmental trajectory of different cell lineages within the diencephalon. This allowed the identification of the genetic cascades and gene regulatory networks underlying the progression of the cell cycle, neurogenesis, and cellular diversification. The analysis provides new insights into the molecular mechanism underlying the specification and amplification of thalamic progenitor cells. In addition, the single-cell-resolved trajectories not only confirm a close relationship between the rostral thalamus and prethalamus, but also uncover an unexpected close relationship between the caudal thalamus, epithalamus and rostral pretectum. Our data provide a useful resource for the systematic study of cell heterogeneity and differentiation kinetics within the developing diencephalon.

scholarly journals Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains

2019 ◽  
Author(s):  
Ekaterina Khrameeva ◽  
Ilia Kurochkin ◽  
Dingding Han ◽  
Patricia Guijarro ◽  
Sabina Kanton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neuronal Cell ◽  
Cell Types ◽  
Brain Regions ◽  
Human Cognition ◽  
Human Lineage ◽  
Cell Type ◽  
Cell Nuclei ◽  
Tissue Samples ◽  
Cell Type Specific

ABSTRACTIdentification of gene expression traits unique to the human brain sheds light on the mechanisms of human cognition. Here we searched for gene expression traits separating humans from other primates by analyzing 88,047 cell nuclei and 422 tissue samples representing 33 brain regions of humans, chimpanzees, bonobos, and macaques. We show that gene expression evolves rapidly within cell types, with more than two-thirds of cell type-specific differences not detected using conventional RNA sequencing of tissue samples. Neurons tend to evolve faster in all hominids, but non-neuronal cell types, such as astrocytes and oligodendrocyte progenitors, show more differences on the human lineage, including alterations of spatial distribution across neocortical layers.

scholarly journals Subcellular proteomics of dopamine neurons in the mouse brain reveals axonal enrichment of proteins encoded by Parkinson's disease-linked genes

2021 ◽  
Author(s):  
Benjamin D. Hobson ◽  
Se Joon Choi ◽  
Rajesh K. Soni ◽  
David Sulzer ◽  
Peter A Sims
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Mouse Brain ◽  
Dopaminergic Neurons ◽  
Cell Biology ◽  
Neuronal Cell ◽  
Cell Types ◽  
Dopamine Neurons ◽  
Cell Type Specificity ◽  
Subcellular Proteomics

Dopaminergic neurons modulate neural circuits and behaviors via dopamine release from expansive, long range axonal projections. The elaborate cytoarchitecture of these neurons is embedded within complex brain tissue, making it difficult to access the neuronal proteome using conventional methods. Here, we demonstrate APEX2 proximity labeling within genetically targeted neurons in the mouse brain, enabling subcellular proteomics with cell type-specificity. By combining APEX2 biotinylation with mass spectrometry, we mapped the somatodendritic and axonal proteomes of midbrain dopaminergic neurons. Our dataset reveals the proteomic architecture underlying proteostasis, axonal metabolism, and neurotransmission in these neurons. We find a significant enrichment of proteins encoded by Parkinson's disease-linked genes in striatal dopaminergic axons, including proteins with previously undescribed axonal localization. These proteomic datasets provide a resource for neuronal cell biology, and this approach can be readily adapted for study of other neural cell types.

scholarly journals Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

2018 ◽  
Author(s):  
Julien Delile ◽  
Teresa Rayon ◽  
Manuela Melchionda ◽  
Amelia Edwards ◽  
James Briscoe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spinal Cord ◽  
Single Cell ◽  
Neural Tube ◽  
Temporal Dynamics ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Neuronal Diversity ◽  
Systematic Analysis ◽  
Neural Tube Development

ABSTRACTThe coordinated spatial and temporal regulation of gene expression in the vertebrate neural tube determines the identity of neural progenitors and the function and physiology of the neurons they generate. Progress has been made deciphering the gene regulatory programmes responsible for this process, however, the complexity of the tissue has hampered the systematic analysis of the network and the underlying mechanisms. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions of the developing mouse neural tube between embryonic days (e)9.5-e13.5. We confirmed the data accurately recapitulates neural tube development, allowing us to identify new markers for specific progenitor and neuronal populations. In addition, the analysis highlighted a previously underappreciated temporal component to the mechanisms generating neuronal diversity and revealed common features in the sequence of transcriptional events that lead to the differentiation of specific neuronal subtypes. Together the data provide a compendium of gene expression for classifying spinal cord cell types that will support future studies of neural tube development, function, and disease.

scholarly journals MANF regulates unfolded protein response and neuronal survival through its ER-located receptor IRE1α

2020 ◽  
Author(s):  
Vera Kovaleva ◽  
Li-Ying Yu ◽  
Larisa Ivanova ◽  
Jinhan Nam ◽  
Ave Eesmaa ◽  
...  
Keyword(s):  
Er Stress ◽  
Unfolded Protein Response ◽  
Neuronal Cell ◽  
Direct Interaction ◽  
Cell Types ◽  
Dopamine Neurons ◽  
Unfolded Protein ◽  
Protein Response

AbstractMesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-located protein with cytoprotective effects in numerous cell types in vitro and in models of neurodegeneration and diabetes in vivo. So far, the exact mode of its action has remained elusive and plasma membrane or ER-located receptors of MANF have not been identified. We have found that MANF can directly interact with transmembrane unfolded protein response (UPR) receptor IRE1α and compete with the major ER chaperone BiP (GRP78) for the interaction with IRE1α. With lower affinities MANF can also interact with other UPR receptors, PERK and ATF6. Using molecular modeling and mutagenesis analysis, we have identified the exact structural MANF regions involved in its binding to the luminal domain of IRE1α. MANF attenuates UPR signaling by decreasing IRE1α oligomerization and IRE1α phosphorylation. MANF mutant deficient in IRE1α binding cannot regulate IRE1α oligomerization and fails to protect neurons from ER stress induced death. Importantly, we found that MANF-IRE1α interaction is also crucial for the survival promoting action of MANF for dopamine neurons in an animal model of Parkinson’s disease. Our data reveal a novel mechanism of IRE1α regulation during ER stress and demonstrate the intracellular mode of action of MANF as a modulator of UPR and neuronal cell survival through the direct interaction with IRE1α and regulation of its activity. Furthermore, our data explain why MANF in contrast to other growth factors has no effects on naive cells and rescues only ER stressed or injured cells.

scholarly journals Molecular, spatial and projection diversity of neurons in primary motor cortex revealed by in situ single-cell transcriptomics

2020 ◽  
Author(s):  
Meng Zhang ◽  
Stephen W. Eichhorn ◽  
Brian Zingg ◽  
Zizhen Yao ◽  
Hongkui Zeng ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Resolution ◽  
Single Cell ◽  
Primary Motor Cortex ◽  
Expression Profiles ◽  
Neuronal Cell ◽  
Gene Expression Profiles ◽  
Cell Types ◽  
Different Cell Types

AbstractA mammalian brain is comprised of numerous cell types organized in an intricate manner to form functional neural circuits. Single-cell RNA sequencing provides a powerful approach to identify cell types based on their gene expression profiles and has revealed many distinct cell populations in the brain1-3. Single-cell epigenomic profiling4,5 further provides information on gene-regulatory signatures of different cell types. Understanding how different cell types contribute to brain function, however, requires knowledge of their spatial organization and connectivity, which is not preserved in sequencing-based methods that involve cell dissociation3,6. Here, we used an in situ single-cell transcriptome-imaging method, multiplexed error-robust fluorescence in situ hybridization (MERFISH)7, to generate a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex (MOp). We profiled ∼300,000 cells in the MOp, identified 95 neuronal and non-neuronal cell clusters, and revealed a complex spatial map in which not only excitatory neuronal clusters but also most inhibitory neuronal clusters adopted layered organizations. Notably, intratelencephalic (IT) cells, the largest branch of neurons in the MOp, formed a continuous spectrum of cells with gradual changes in both gene expression profiles and cortical depth positions in a highly correlated manner. Furthermore, we integrated MERFISH with retrograde tracing to probe the projection targets for different MOp neuronal cell types and found that projections of MOp neurons to other cortical regions formed a many-to-many network with each target region receiving input preferentially from a different composition of IT clusters. Overall, our results provide a high-resolution spatial and projection map of molecularly defined cell types in the MOp. We anticipate that the imaging platform described here can be broadly applied to create high-resolution cell atlases of a wide range of systems.

Sign in / Sign up

Export Citation Format

Share Document