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1.
Elife ; 92020 04 07.
Article in English | MEDLINE | ID: mdl-32255422

ABSTRACT

Wiring a complex brain requires many neurons with intricate cell specificity, generated by a limited number of neural stem cells. Drosophila central brain lineages are a predetermined series of neurons, born in a specific order. To understand how lineage identity translates to neuron morphology, we mapped 18 Drosophila central brain lineages. While we found large aggregate differences between lineages, we also discovered shared patterns of morphological diversification. Lineage identity plus Notch-mediated sister fate govern primary neuron trajectories, whereas temporal fate diversifies terminal elaborations. Further, morphological neuron types may arise repeatedly, interspersed with other types. Despite the complexity, related lineages produce similar neuron types in comparable temporal patterns. Different stem cells even yield two identical series of dopaminergic neuron types, but with unrelated sister neurons. Together, these phenomena suggest that straightforward rules drive incredible neuronal complexity, and that large changes in morphology can result from relatively simple fating mechanisms.


Subject(s)
Brain/physiology , Cell Lineage , Drosophila melanogaster/cytology , Neural Stem Cells/cytology , Neurogenesis , Animals , Brain/cytology , Drosophila melanogaster/genetics , Larva , Neurons/cytology
2.
Nucleic Acids Res ; 48(8): 4344-4356, 2020 05 07.
Article in English | MEDLINE | ID: mdl-32187363

ABSTRACT

The genome is the blueprint for an organism. Interrogating the genome, especially locating critical cis-regulatory elements, requires deletion analysis. This is conventionally performed using synthetic constructs, making it cumbersome and non-physiological. Thus, we created Cas9-mediated Arrayed Mutagenesis of Individual Offspring (CAMIO) to achieve comprehensive analysis of a targeted region of native DNA. CAMIO utilizes CRISPR that is spatially restricted to generate independent deletions in the intact Drosophila genome. Controlled by recombination, a single guide RNA is stochastically chosen from a set targeting a specific DNA region. Combining two sets increases variability, leading to either indels at 1-2 target sites or inter-target deletions. Cas9 restriction to male germ cells elicits autonomous double-strand-break repair, consequently creating offspring with diverse mutations. Thus, from a single population cross, we can obtain a deletion matrix covering a large expanse of DNA at both coarse and fine resolution. We demonstrate the ease and power of CAMIO by mapping 5'UTR sequences crucial for chinmo's post-transcriptional regulation.


Subject(s)
CRISPR-Cas Systems , Drosophila/genetics , Gene Editing , Mutagenesis , 5' Untranslated Regions , Animals , Animals, Genetically Modified , CRISPR-Associated Protein 9 , Drosophila Proteins/genetics , Genome, Insect , INDEL Mutation , Male , Nerve Tissue Proteins/genetics , Spermatozoa/metabolism
3.
Elife ; 92020 01 08.
Article in English | MEDLINE | ID: mdl-31913118

ABSTRACT

Inner ear cochlear spiral ganglion neurons (SGNs) transmit sound information to the brainstem. Recent single cell RNA-Seq studies have revealed heterogeneities within SGNs. Nonetheless, much remains unknown about the transcriptome of SGNs, especially which genes are specifically expressed in SGNs. To address these questions, we needed a deeper and broader gene coverage than that in previous studies. We performed bulk RNA-Seq on mouse SGNs at five ages, and on two reference cell types (hair cells and glia). Their transcriptome comparison identified genes previously unknown to be specifically expressed in SGNs. To validate our dataset and provide useful genetic tools for this research field, we generated two knockin mouse strains: Scrt2-P2A-tdTomato and Celf4-3xHA-P2A-iCreER-T2A-EGFP. Our comprehensive analysis confirmed the SGN-selective expression of the candidate genes, testifying to the quality of our transcriptome data. These two mouse strains can be used to temporally label SGNs or to sort them.


Subject(s)
Aging/genetics , Gene Expression Profiling , Gene Expression , Neurons/metabolism , Spiral Ganglion/cytology , Transcriptome , Animals , Brain/metabolism , CELF Proteins/genetics , Gene Knock-In Techniques , Mice , RNA-Seq , Spiral Ganglion/embryology , Spiral Ganglion/metabolism
4.
Elife ; 82019 09 23.
Article in English | MEDLINE | ID: mdl-31545163

ABSTRACT

Temporal patterning is a seminal method of expanding neuronal diversity. Here we unravel a mechanism decoding neural stem cell temporal gene expression and transforming it into discrete neuronal fates. This mechanism is characterized by hierarchical gene expression. First, Drosophila neuroblasts express opposing temporal gradients of RNA-binding proteins, Imp and Syp. These proteins promote or inhibit chinmo translation, yielding a descending neuronal gradient. Together, first and second-layer temporal factors define a temporal expression window of BTB-zinc finger nuclear protein, Mamo. The precise temporal induction of Mamo is achieved via both transcriptional and post-transcriptional regulation. Finally, Mamo is essential for the temporally defined, terminal identity of α'/ß' mushroom body neurons and identity maintenance. We describe a straightforward paradigm of temporal fate specification where diverse neuronal fates are defined via integrating multiple layers of gene regulation. The neurodevelopmental roles of orthologous/related mammalian genes suggest a fundamental conservation of this mechanism in brain development.


Subject(s)
Brain/growth & development , Cell Differentiation , DNA-Binding Proteins/metabolism , Drosophila Proteins/metabolism , Gene Expression Regulation , Gene Regulatory Networks , Neural Stem Cells/physiology , Neurons/physiology , Transcription Factors/metabolism , Animals , Drosophila , Gene Expression Profiling
5.
Elife ; 82019 04 12.
Article in English | MEDLINE | ID: mdl-30977723

ABSTRACT

Understanding the principles governing neuronal diversity is a fundamental goal for neuroscience. Here, we provide an anatomical and transcriptomic database of nearly 200 genetically identified cell populations. By separately analyzing the robustness and pattern of expression differences across these cell populations, we identify two gene classes contributing distinctly to neuronal diversity. Short homeobox transcription factors distinguish neuronal populations combinatorially, and exhibit extremely low transcriptional noise, enabling highly robust expression differences. Long neuronal effector genes, such as channels and cell adhesion molecules, contribute disproportionately to neuronal diversity, based on their patterns rather than robustness of expression differences. By linking transcriptional identity to genetic strains and anatomical atlases, we provide an extensive resource for further investigation of mouse neuronal cell types.


Subject(s)
Brain/anatomy & histology , Brain/cytology , Gene Expression Profiling , Neurons/physiology , Animals , Mice
6.
PLoS Genet ; 14(7): e1007552, 2018 07.
Article in English | MEDLINE | ID: mdl-30063705

ABSTRACT

In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/metabolism , Cellular Reprogramming/genetics , Hair Cells, Auditory/physiology , LIM-Homeodomain Proteins/metabolism , Regeneration/genetics , Transcription Factors/metabolism , Animals , Animals, Newborn , Basic Helix-Loop-Helix Transcription Factors/genetics , Gene Expression Profiling/methods , LIM-Homeodomain Proteins/genetics , Mice , Mice, Inbred C57BL , Mice, Transgenic , Sequence Analysis, RNA/methods , Single-Cell Analysis/methods , Transcription Factors/genetics
7.
Curr Biol ; 27(9): 1303-1313, 2017 May 08.
Article in English | MEDLINE | ID: mdl-28434858

ABSTRACT

Building a sizable, complex brain requires both cellular expansion and diversification. One mechanism to achieve these goals is production of multiple transiently amplifying intermediate neural progenitors (INPs) from a single neural stem cell. Like mammalian neural stem cells, Drosophila type II neuroblasts utilize INPs to produce neurons and glia. Within a given lineage, the consecutively born INPs produce morphologically distinct progeny, presumably due to differential inheritance of temporal factors. To uncover the underlying temporal fating mechanisms, we profiled type II neuroblasts' transcriptome across time. Our results reveal opposing temporal gradients of Imp and Syp RNA-binding proteins (descending and ascending, respectively). Maintaining high Imp throughout serial INP production expands the number of neurons and glia with early temporal fate at the expense of cells with late fate. Conversely, precocious upregulation of Syp reduces the number of cells with early fate. Furthermore, we reveal that the transcription factor Seven-up initiates progression of the Imp/Syp gradients. Interestingly, neuroblasts that maintain initial Imp/Syp levels can still yield progeny with a small range of early fates. We therefore propose that the Seven-up-initiated Imp/Syp gradients create coarse temporal windows within type II neuroblasts to pattern INPs, which subsequently undergo fine-tuned subtemporal patterning.


Subject(s)
DNA-Binding Proteins/metabolism , Drosophila Proteins/metabolism , Drosophila melanogaster/growth & development , Gene Expression Regulation, Developmental , Neural Stem Cells/metabolism , RNA-Binding Proteins/metabolism , Receptors, Steroid/metabolism , Animals , Cell Cycle , Cell Lineage , Cell Proliferation , Drosophila melanogaster/metabolism , Gene Expression Profiling , Neurogenesis , Neurons/cytology , Neurons/metabolism , Stem Cell Factor/metabolism
8.
Cell Rep ; 16(10): 2711-2722, 2016 09 06.
Article in English | MEDLINE | ID: mdl-27568566

ABSTRACT

Synaptic scaling is a form of homeostatic plasticity driven by transcription-dependent changes in AMPA-type glutamate receptor (AMPAR) trafficking. To uncover the pathways involved, we performed a cell-type-specific screen for transcripts persistently altered during scaling, which identified the µ subunit (µ3A) of the adaptor protein complex AP-3A. Synaptic scaling increased µ3A (but not other AP-3 subunits) in pyramidal neurons and redistributed dendritic µ3A and AMPAR to recycling endosomes (REs). Knockdown of µ3A prevented synaptic scaling and this redistribution, while overexpression (OE) of full-length µ3A or a truncated µ3A that cannot interact with the AP-3A complex was sufficient to drive AMPAR to REs. Finally, OE of µ3A acted synergistically with GRIP1 to recruit AMPAR to the dendritic membrane. These data suggest that excess µ3A acts independently of the AP-3A complex to reroute AMPAR to RE, generating a reservoir of receptors essential for the regulated recruitment to the synaptic membrane during scaling up.


Subject(s)
Adaptor Protein Complex 3/metabolism , Adaptor Protein Complex mu Subunits/metabolism , Endosomes/metabolism , Homeostasis , Neuronal Plasticity/physiology , Receptors, AMPA/metabolism , Up-Regulation , Adaptor Proteins, Signal Transducing/metabolism , Animals , Dendrites/metabolism , Discs Large Homolog 1 Protein/metabolism , Endocytosis , Gene Knockdown Techniques , Mice , Nerve Tissue Proteins/metabolism , Pyramidal Cells/metabolism , Synapses/metabolism , Transcriptome/genetics
9.
Cell ; 165(7): 1749-1761, 2016 Jun 16.
Article in English | MEDLINE | ID: mdl-27315482

ABSTRACT

Neurons are well suited for computations on millisecond timescales, but some neuronal circuits set behavioral states over long time periods, such as those involved in energy homeostasis. We found that multiple types of hypothalamic neurons, including those that oppositely regulate body weight, are specialized as near-perfect synaptic integrators that summate inputs over extended timescales. Excitatory postsynaptic potentials (EPSPs) are greatly prolonged, outlasting the neuronal membrane time-constant up to 10-fold. This is due to the voltage-gated sodium channel Nav1.7 (Scn9a), previously associated with pain-sensation but not synaptic integration. Scn9a deletion in AGRP, POMC, or paraventricular hypothalamic neurons reduced EPSP duration, synaptic integration, and altered body weight in mice. In vivo whole-cell recordings in the hypothalamus confirmed near-perfect synaptic integration. These experiments show that integration of synaptic inputs over time by Nav1.7 is critical for body weight regulation and reveal a mechanism for synaptic control of circuits regulating long term homeostatic functions.


Subject(s)
Body Weight Maintenance , Hypothalamus/cytology , NAV1.7 Voltage-Gated Sodium Channel/metabolism , Neurons/metabolism , Synapses , Agouti-Related Protein/metabolism , Animals , Homeostasis , Hypothalamus/metabolism , Male , Mice , Mice, Transgenic
10.
Elife ; 5: e14997, 2016 Apr 26.
Article in English | MEDLINE | ID: mdl-27113915

ABSTRACT

Clarifying gene expression in narrowly defined neuronal populations can provide insight into cellular identity, computation, and functionality. Here, we used next-generation RNA sequencing (RNA-seq) to produce a quantitative, whole genome characterization of gene expression for the major excitatory neuronal classes of the hippocampus; namely, granule cells and mossy cells of the dentate gyrus, and pyramidal cells of areas CA3, CA2, and CA1. Moreover, for the canonical cell classes of the trisynaptic loop, we profiled transcriptomes at both dorsal and ventral poles, producing a cell-class- and region-specific transcriptional description for these populations. This dataset clarifies the transcriptional properties and identities of lesser-known cell classes, and moreover reveals unexpected variation in the trisynaptic loop across the dorsal-ventral axis. We have created a public resource, Hipposeq (http://hipposeq.janelia.org), which provides analysis and visualization of these data and will act as a roadmap relating molecules to cells, circuits, and computation in the hippocampus.


Subject(s)
Databases, Nucleic Acid , Hippocampus/physiology , Neurons/physiology , Transcriptome , Animals , High-Throughput Nucleotide Sequencing , Mice, Inbred C57BL , Mice, Transgenic
11.
Elife ; 5: e13503, 2016 Mar 21.
Article in English | MEDLINE | ID: mdl-26999799

ABSTRACT

There is a continuing need for driver strains to enable cell-type-specific manipulation in the nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. However, since genes are often expressed in many cell types, many of these lines have relatively broad expression patterns. We report an alternative transgenic approach capturing distal enhancers for more focused expression. We identified an enhancer trap probe often producing restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac transposon. We established more than 200 lines and found many lines that label small subsets of neurons in brain substructures, including known and novel cell types. Images and other information about each line are available online (enhancertrap.bio.brandeis.edu).


Subject(s)
Molecular Biology/methods , Neurobiology/methods , Neurons/physiology , Staining and Labeling/methods , Animals , Mice , Mice, Transgenic
12.
Neuron ; 89(2): 351-68, 2016 Jan 20.
Article in English | MEDLINE | ID: mdl-26777276

ABSTRACT

Tissue and organ function has been conventionally understood in terms of the interactions among discrete and homogeneous cell types. This approach has proven difficult in neuroscience due to the marked diversity across different neuron classes, but it may be further hampered by prominent within-class variability. Here, we considered a well-defined canonical neuronal population­hippocampal CA1 pyramidal cells (CA1 PCs)­and systematically examined the extent and spatial rules of transcriptional heterogeneity. Using next-generation RNA sequencing, we identified striking variability in CA1 PCs, such that the differences within CA1 along the dorsal-ventral axis rivaled differences across distinct pyramidal neuron classes. This variability emerged from a spectrum of continuous gene-expression gradients, producing a transcriptional profile consistent with a multifarious continuum of cells. This work reveals an unexpected amount of variability within a canonical and narrowly defined neuronal population and suggests that continuous, within-class heterogeneity may be an important feature of neural circuits.


Subject(s)
CA1 Region, Hippocampal/cytology , CA1 Region, Hippocampal/physiology , Gene Expression Profiling/methods , Pyramidal Cells/physiology , Animals , Female , Gene Expression Regulation , Male , Mice , Mice, Transgenic , Organ Culture Techniques
13.
Development ; 143(3): 411-21, 2016 Feb 01.
Article in English | MEDLINE | ID: mdl-26700685

ABSTRACT

A brain consists of numerous distinct neurons arising from a limited number of progenitors, called neuroblasts in Drosophila. Each neuroblast produces a specific neuronal lineage. To unravel the transcriptional networks that underlie the development of distinct neuroblast lineages, we marked and isolated lineage-specific neuroblasts for RNA sequencing. We labeled particular neuroblasts throughout neurogenesis by activating a conditional neuroblast driver in specific lineages using various intersection strategies. The targeted neuroblasts were efficiently recovered using a custom-built device for robotic single-cell picking. Transcriptome analysis of mushroom body, antennal lobe and type II neuroblasts compared with non-selective neuroblasts, neurons and glia revealed a rich repertoire of transcription factors expressed among neuroblasts in diverse patterns. Besides transcription factors that are likely to be pan-neuroblast, many transcription factors exist that are selectively enriched or repressed in certain neuroblasts. The unique combinations of transcription factors present in different neuroblasts may govern the diverse lineage-specific neuron fates.


Subject(s)
Cell Lineage/genetics , Drosophila melanogaster/genetics , Gene Targeting , Neurons/cytology , Robotics , Transcriptome/genetics , Animals , Animals, Genetically Modified , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/cytology , Gene Expression Regulation, Developmental , Sequence Analysis, RNA , Single-Cell Analysis , Transcription Factors/metabolism
14.
Science ; 350(6258): 317-20, 2015 Oct 16.
Article in English | MEDLINE | ID: mdl-26472907

ABSTRACT

Neural stem cells show age-dependent developmental potentials, as evidenced by their production of distinct neuron types at different developmental times. Drosophila neuroblasts produce long, stereotyped lineages of neurons. We searched for factors that could regulate neural temporal fate by RNA-sequencing lineage-specific neuroblasts at various developmental times. We found that two RNA-binding proteins, IGF-II mRNA-binding protein (Imp) and Syncrip (Syp), display opposing high-to-low and low-to-high temporal gradients with lineage-specific temporal dynamics. Imp and Syp promote early and late fates, respectively, in both a slowly progressing and a rapidly changing lineage. Imp and Syp control neuronal fates in the mushroom body lineages by regulating the temporal transcription factor Chinmo translation. Together, the opposing Imp/Syp gradients encode stem cell age, specifying multiple cell fates within a lineage.


Subject(s)
Cell Lineage , Drosophila Proteins/physiology , Drosophila melanogaster/growth & development , Neural Stem Cells/cytology , Neurogenesis/physiology , Neurons/cytology , RNA-Binding Proteins/physiology , Animals , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Drosophila melanogaster/genetics , Mushroom Bodies/cytology , Mushroom Bodies/growth & development , Nerve Tissue Proteins/metabolism , Neurogenesis/genetics , RNA-Binding Proteins/genetics , Sequence Analysis, RNA
15.
Elife ; 42015 Sep 02.
Article in English | MEDLINE | ID: mdl-26329458

ABSTRACT

Molecular and cellular processes in neurons are critical for sensing and responding to energy deficit states, such as during weight-loss. Agouti related protein (AGRP)-expressing neurons are a key hypothalamic population that is activated during energy deficit and increases appetite and weight-gain. Cell type-specific transcriptomics can be used to identify pathways that counteract weight-loss, and here we report high-quality gene expression profiles of AGRP neurons from well-fed and food-deprived young adult mice. For comparison, we also analyzed Proopiomelanocortin (POMC)-expressing neurons, an intermingled population that suppresses appetite and body weight. We find that AGRP neurons are considerably more sensitive to energy deficit than POMC neurons. Furthermore, we identify cell type-specific pathways involving endoplasmic reticulum-stress, circadian signaling, ion channels, neuropeptides, and receptors. Combined with methods to validate and manipulate these pathways, this resource greatly expands molecular insight into neuronal regulation of body weight, and may be useful for devising therapeutic strategies for obesity and eating disorders.


Subject(s)
Gene Expression Profiling , Hypothalamus/physiology , Sensory Receptor Cells/physiology , Weight Loss , Agouti-Related Protein/analysis , Animals , Hypothalamus/cytology , Mice , Pro-Opiomelanocortin/analysis , Sensory Receptor Cells/chemistry
16.
J Neurosci ; 34(38): 12877-83, 2014 Sep 17.
Article in English | MEDLINE | ID: mdl-25232122

ABSTRACT

Mutations in methyl-CpG-binding protein 2 (MeCP2) cause Rett syndrome and related autism spectrum disorders (Amir et al., 1999). MeCP2 is believed to be required for proper regulation of brain gene expression, but prior microarray studies in Mecp2 knock-out mice using brain tissue homogenates have revealed only subtle changes in gene expression (Tudor et al., 2002; Nuber et al., 2005; Jordan et al., 2007; Chahrour et al., 2008). Here, by profiling discrete subtypes of neurons we uncovered more dramatic effects of MeCP2 on gene expression, overcoming the "dilution problem" associated with assaying homogenates of complex tissues. The results reveal misregulation of genes involved in neuronal connectivity and communication. Importantly, genes upregulated following loss of MeCP2 are biased toward longer genes but this is not true for downregulated genes, suggesting MeCP2 may selectively repress long genes. Because genes involved in neuronal connectivity and communication, such as cell adhesion and cell-cell signaling genes, are enriched among longer genes, their misregulation following loss of MeCP2 suggests a possible etiology for altered circuit function in Rett syndrome.


Subject(s)
Down-Regulation/genetics , Methyl-CpG-Binding Protein 2/metabolism , Neurons/metabolism , Animals , Cell Adhesion/genetics , Cell Communication/genetics , Disease Models, Animal , Gene Expression Profiling , Male , Mice , Mice, Knockout , Mice, Transgenic , Oligonucleotide Array Sequence Analysis , Organ Specificity , Rett Syndrome/genetics
17.
Proc Natl Acad Sci U S A ; 111(31): 11515-20, 2014 Aug 05.
Article in English | MEDLINE | ID: mdl-25049382

ABSTRACT

Asthma is a common debilitating inflammatory lung disease affecting over 200 million people worldwide. Here, we investigated neurogenic components involved in asthmatic-like attacks using the ovalbumin-sensitized murine model of the disease, and identified a specific population of neurons that are required for airway hyperreactivity. We show that ablating or genetically silencing these neurons abolished the hyperreactive broncho-constrictions, even in the presence of a fully developed lung inflammatory immune response. These neurons are found in the vagal ganglia and are characterized by the expression of the transient receptor potential vanilloid 1 (TRPV1) ion channel. However, the TRPV1 channel itself is not required for the asthmatic-like hyperreactive airway response. We also demonstrate that optogenetic stimulation of this population of TRP-expressing cells with channelrhodopsin dramatically exacerbates airway hyperreactivity of inflamed airways. Notably, these cells express the sphingosine-1-phosphate receptor 3 (S1PR3), and stimulation with a S1PR3 agonist efficiently induced broncho-constrictions, even in the absence of ovalbumin sensitization and inflammation. Our results show that the airway hyperreactivity phenotype can be physiologically dissociated from the immune component, and provide a platform for devising therapeutic approaches to asthma that target these pathways separately.


Subject(s)
Asthma/pathology , Asthma/physiopathology , Bronchial Hyperreactivity/pathology , Bronchial Hyperreactivity/physiopathology , Pneumonia/pathology , Respiratory System/innervation , Sensory Receptor Cells/pathology , Animals , Asthma/complications , Bronchial Hyperreactivity/complications , Gene Deletion , Gene Silencing , Mice , Mice, Inbred C57BL , Pneumonia/complications , Pneumonia/physiopathology , Receptors, Lysosphingolipid/metabolism , Respiratory System/pathology , Respiratory System/physiopathology , Sensory Receptor Cells/metabolism , TRPV Cation Channels/metabolism , Vagus Nerve/metabolism , Vagus Nerve/pathology
18.
Proc Natl Acad Sci U S A ; 111(14): 5397-402, 2014 Apr 08.
Article in English | MEDLINE | ID: mdl-24706869

ABSTRACT

Spatial patterns of gene expression in the vertebrate brain are not independent, as pairs of genes can exhibit complex patterns of coexpression. Two genes may be similarly expressed in one region, but differentially expressed in other regions. These correlations have been studied quantitatively, particularly for the Allen Atlas of the adult mouse brain, but their biological meaning remains obscure. We propose a simple model of the coexpression patterns in terms of spatial distributions of underlying cell types and establish its plausibility using independently measured cell-type-specific transcriptomes. The model allows us to predict the spatial distribution of cell types in the mouse brain.


Subject(s)
Brain/metabolism , Gene Expression , Models, Biological , Animals , Mice
19.
Elife ; 2: e00400, 2013 Feb 26.
Article in English | MEDLINE | ID: mdl-23467508

ABSTRACT

Cerebellar granule cells constitute the majority of neurons in the brain and are the primary conveyors of sensory and motor-related mossy fiber information to Purkinje cells. The functional capability of the cerebellum hinges on whether individual granule cells receive mossy fiber inputs from multiple precerebellar nuclei or are instead unimodal; this distinction is unresolved. Using cell-type-specific projection mapping with synaptic resolution, we observed the convergence of separate sensory (upper body proprioceptive) and basilar pontine pathways onto individual granule cells and mapped this convergence across cerebellar cortex. These findings inform the long-standing debate about the multimodality of mammalian granule cells and substantiate their associative capacity predicted in the Marr-Albus theory of cerebellar function. We also provide evidence that the convergent basilar pontine pathways carry corollary discharges from upper body motor cortical areas. Such merging of related corollary and sensory streams is a critical component of circuit models of predictive motor control. DOI:http://dx.doi.org/10.7554/eLife.00400.001.


Subject(s)
Cerebellum/physiology , Motor Activity , Nerve Fibers/physiology , Neurons/physiology , Pons/physiology , Proprioception , Animals , Cerebellum/cytology , Cerebellum/metabolism , Feedback, Sensory , Mice, Inbred C57BL , Mice, Transgenic , Nerve Fibers/metabolism , Neural Pathways/physiology , Neuroanatomical Tract-Tracing Techniques , Neurons/metabolism , Pons/cytology , Pons/metabolism , Synaptic Transmission
20.
Expert Rev Proteomics ; 8(5): 591-604, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21999830

ABSTRACT

Single-cell analysis is gaining popularity in the field of mass spectrometry as a method for analyzing protein and peptide content in cells. The spatial resolution of MALDI mass spectrometry (MS) imaging is by a large extent limited by the laser focal diameter and the displacement of analytes during matrix deposition. Owing to recent advancements in both laser optics and matrix deposition methods, spatial resolution on the order of a single eukaryotic cell is now achievable by MALDI MS imaging. Provided adequate instrument sensitivity, a lateral resolution of approximately 10 µm is currently attainable with commercial instruments. As a result of these advances, MALDI MS imaging is poised to become a transformative clinical technology. In this article, the crucial steps needed to obtain single-cell resolution are discussed, as well as potential applications to disease research.


Subject(s)
Biomarkers/analysis , Proteins/analysis , Single-Cell Analysis/methods , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Animals , Diagnostic Imaging , Humans , Immunohistochemistry/methods , Prognosis
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