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

eLife ◽  
2019 ◽  
Vol 8 ◽  
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.

scholarly journals FMRP binding to a ranked subset of long genes is revealed by coupled CLIP and TRAP in specific neuronal cell types

2019 ◽  
Author(s):  
Sarah J. Van Driesche ◽  
Kirsty Sawicka ◽  
Chaolin Zhang ◽  
Sharon K.Y. Hung ◽  
Christopher Y. Park ◽  
...  
Keyword(s):  
Purkinje Cells ◽  
Fragile X ◽  
Neuronal Cell ◽  
Transcript Abundance ◽  
Cell Types ◽  
Loss Of Function ◽  
Ip3 Receptor ◽  
Mrna Targets ◽  
Ranked List

SummaryLoss of function of the Fragile X Mental Retardation Protein (FMRP) in human Fragile X Syndrome (FXS) and in model organisms results in phenotypes of abnormal neuronal structure and dynamics, synaptic function and connectivity which may contribute to a state of neuronal, circuit and organism hyperexcitability. Previousin vivoidentification of FMRP association with specific mRNA targets in mouse brain revealed that FMRP regulates the translation of a large fraction of the synaptic proteome in both pre- and post-synaptic compartments as well as many transcription factors and chromatin modifying proteins. However, it was not previously possible to determine the ratio of FMRP binding to transcript abundance due to the complexity of different neuronal cell types in whole brain. Moreover, it has been difficult to link the translational regulation of specific targets to model phenotypes or human symptoms. For example, loss-of-function of FMRP in the Purkinje cells of the cerebellum results in three cell autonomous phenotypes related to learning and memory, including enhanced mGluR-LTD at parallel fiber synapses, altered dendritic spines and behavioral deficits in a eyeblink-conditioning learning paradigm shared by human FXS patients. The molecular basis for these and related human Fragile X phenotypes is unknown. To address these critical issues we have developed a new mouse model (theFmr1cTAG mouse) in which endogenous FMRP can be conditionally tagged for RNA:protein crosslinking and immunoprecipitation (CLIP) identification of the RNAs with which it interactsin vivo. We used theFmr1cTAG mouse to quantitatively evaluate FMRP-mRNA association in Purkinje and cerebellar granule neurons which together comprise the parallel-fiber synapse. We calculated a stoichiometrically ranked list of FMRP RNA binding events by normalizing to ribosome-associated transcript abundance determined by TRAP-seq, and now definitively find that FMRP associates with specific sets of mRNAs which differ between the two cell types. In Purkinje cells, many components of the mGluR signaling pathway are FMRP targets including the top-ranked Purkinje cell mRNAItpr1, encoding the IP3 receptor, the function of which is critical to proper mGluR-dependent synaptic plasticity. In sum, this novel approach provides the first ranked list of FMRP target mRNAs and further reveals that FMRP regulates a specific set of long neural genes related to relevant cell autonomous phenotypes.HighlightsWe have created a mouse model in which endogenous FMRP can be conditionally tagged.Using tag-specific CLIP we describe ranked and specific sets ofin vivoFMRP mRNA targets in two types of neurons.This ranking was used to reveal that FMRP regulates mRNAs with long coding sequences.FMRP mRNA targets in Purkinje cells, including the top-ranked IP3 receptor, are related to cell-autonomous Fragile X phenotypes.We have updated our previous list of whole mouse brain FMRP mRNA targets with more replicates, deeper sequencing and improved analysisThe use of tagged FMRP in less abundant cell populations allowed identification of novel mRNA targets missed in a whole brain analysis

scholarly journals Extracellular spike waveform dissociates four functionally distinct cell classes in primate cortex

2019 ◽  
Author(s):  
Caterina Trainito ◽  
Constantin von Nicolai ◽  
Earl K. Miller ◽  
Markus Siegel
Keyword(s):  
Visual Information ◽  
Neuronal Cell ◽  
Cell Types ◽  
Brain Regions ◽  
Frontal Eye Field ◽  
Visual Response ◽  
Cell Type ◽  
Response Dynamics ◽  
Distinct Cell ◽  
Behaving Monkeys

SummaryUnderstanding the function of different neuronal cell types is key to understanding brain function. However, cell type diversity is typically overlooked in electrophysiological studies in awake behaving animals. Here, we show that four functionally distinct cell classes can be robustly identified from extracellular recordings in several cortical regions of awake behaving monkeys. We recorded extracellular spiking activity from dorsolateral prefrontal cortex (dlPFC), the frontal eye field (FEF), and the lateral intraparietal area of macaque monkeys during a visuomotor decision-making task. We employed unsupervised clustering of spike waveforms, which robustly dissociated four distinct cell classes across all three brain regions. The four cell classes were functionally distinct. They showed different baseline firing statistics, visual response dynamics, and coding of visual information. While cell class-specific baseline statistics were consistent across brain regions, response dynamics and information coding were regionally specific. Our results identify four waveform-based cell classes in primate cortex. This opens a new window to dissect and study the cell-type specific function of cortical circuits.

scholarly journals FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons

2021 ◽  
Author(s):  
Caryn R Hale ◽  
Kirsty Sawicka ◽  
Kevin Mora ◽  
John J Fak ◽  
Jin Joo Kang ◽  
...  
Keyword(s):  
Pyramidal Neurons ◽  
Neuronal Cell ◽  
Synaptic Proteins ◽  
Translational Repression ◽  
Functional Modules ◽  
Cell Type ◽  
Ca1 Pyramidal Neurons ◽  
Splicing Isoforms ◽  
Activity Dependent ◽  
Ribosome Association

Neurons are believed to rely on dendritic localization and translation of mRNAs in order to generate activity-dependent changes in the synaptic plasticity. Here, we develop a strategy combining compartment-specific CLIP and TRAP in conditionally tagged mice to precisely define the ribosome bound dendritic transcriptome of CA1 pyramidal neurons. This revealed transcripts that have differentially localized alternative 3′UTR and splicing isoforms. FMRP targets are overrepresented among dendritic mRNAs, and compartment-specific FMRP-CLIP defined 383 dendritic FMRP targets, and also allowed for segregation of whole-cell FMRP targets into functional modules that are locally regulated by FMRP. In the absence of FMRP, dendritic FMRP targets show increased ribosome association, consistent with reported roles for FMRP in translational repression. Together, the data support a model in which distinct patterns of FMRP localization allow it to differentially regulate the expression of nuclear proteins and synaptic proteins within different compartments of a single neuronal cell type.

scholarly journals FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Caryn R Hale ◽  
Kirsty Sawicka ◽  
Kevin Mora ◽  
John J Fak ◽  
Jin Joo Kang ◽  
...  
Keyword(s):  
Cell Body ◽  
Pyramidal Neurons ◽  
Neuronal Cell ◽  
Alternative Polyadenylation ◽  
Cell Type ◽  
Mrna Isoforms ◽  
Protein Coding ◽  
Ca1 Pyramidal Neurons ◽  
Synaptic Functions ◽  
Cell Type Specific

Neurons rely on translation of synaptic mRNAs in order to generate activity-dependent changes in plasticity. Here we develop a strategy combining compartment-specific CLIP and TRAP in conditionally tagged mice to precisely define the ribosome-bound dendritic transcriptome of CA1 pyramidal neurons. We identify CA1 dendritic transcripts with differentially localized mRNA isoforms generated by alternative polyadenylation and alternative splicing, including many which have altered protein-coding capacity. Among dendritic mRNAs, FMRP targets were found to be overrepresented. Cell-type specific FMRP-CLIP and TRAP in microdissected CA1 neuropil revealed 383 dendritic FMRP targets and suggests that FMRP differentially regulates functionally distinct modules in CA1 dendrites and cell bodies. FMRP regulates ~15-20% of mRNAs encoding synaptic functions and 10% of chromatin modulators, in the dendrite and cell body, respectively. In the absence of FMRP, dendritic FMRP targets had increased ribosome association, consistent with a function for FMRP in synaptic translational repression. Conversely, downregulation of FMRP targets involved in chromatin regulation in cell bodies and suggest a role for FMRP in stabilizing mRNAs containing stalled ribosomes in this compartment. Together, the data support a model in which FMRP regulates the translation and expression of synaptic and nuclear proteins within different compartments of a single neuronal cell type.

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 Transcriptional and cell type profiles of cortical brain regions showing ultradian cortisol rhythm dependent responses to emotional face stimulation

2022 ◽  
Author(s):  
Philippe C Habets ◽  
Konstantinos Kalafatakis ◽  
Oleh Dzyubachyk ◽  
Steven van der Werff ◽  
Arlin Keo ◽  
...  
Keyword(s):  
Emotional Processing ◽  
Experimental Studies ◽  
Neuronal Cell ◽  
Cell Types ◽  
Brain Regions ◽  
Specific Cell ◽  
Protein Signaling ◽  
Cell Type ◽  
Endogenous Circadian Rhythm ◽  
Significant Enrichment

The characteristic endogenous circadian rhythm of plasma glucocorticoid concentrations is made up from an underlying ultradian pulsatile secretory pattern. Recent evidence has indicated that this ultradian cortisol pulsatility is crucial for normal emotional response in man. In this study, we investigate the anatomical transcriptional and cell type signature of brain regions sensitive to a loss of ultradian rhythmicity in the context of emotional processing. We combine human cell type and transcriptomic atlas data of high spatial resolution with functional magnetic resonance imaging (fMRI) data. We show that the loss of cortisol ultradian rhythm alters emotional processing response in cortical brain areas that are characterized by transcriptional and cellular profiles of GABAergic function. We find that two previously identified key components of rapid non-genomic GC signaling - the ANXA1 gene and retrograde endocannabinoid signaling - show top differential expression and the most significant enrichment. Our results further indicate that specific cell types, including a specific NPY-expressing GABAergic neuronal cell type, and specific G protein signaling cascades underly the cerebral effects of a loss of ultradian cortisol rhythm. Our results provide a biological mechanistic underpinning of our fMRI findings, indicating specific cell types and cascades as a target for manipulation in future experimental studies.

scholarly journals Cell Type-Specific mRNA Dysregulation in Hippocampal CA1 Pyramidal Neurons of the Fragile X Syndrome Mouse Model

2017 ◽  
Vol 10 ◽  
Author(s):  
Laura Ceolin ◽  
Nathalie Bouquier ◽  
Jihane Vitre-Boubaker ◽  
Stéphanie Rialle ◽  
Dany Severac ◽  
...  
Keyword(s):  
Mouse Model ◽  
Fragile X Syndrome ◽  
Pyramidal Neurons ◽  
Fragile X ◽  
Cell Type ◽  
Ca1 Pyramidal Neurons ◽  
Hippocampal Ca1 ◽  
Cell Type Specific ◽  
Specific Mrna

scholarly journals An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

2020 ◽  
Author(s):  
Yang Eric Li ◽  
Sebastian Preissl ◽  
Xiaomeng Hou ◽  
Ziyang Zhang ◽  
Kai Zhang ◽  
...  
Keyword(s):  
Target Genes ◽  
Adult Mouse ◽  
Neuronal Cell ◽  
Cell Types ◽  
Regulatory Elements ◽  
Brain Regions ◽  
Brain Cell ◽  
Mammalian Brain ◽  
Cell Type ◽  
Gene Regulatory

ABSTRACTThe mammalian cerebrum performs high level sensory, motor control and cognitive functions through highly specialized cortical networks and subcortical nuclei. Recent surveys of mouse and human brains with single cell transcriptomics1–3 and high-throughput imaging technologies4,5 have uncovered hundreds of neuronal cell types and a variety of non-neuronal cell types distributed in different brain regions, but the cell-type-specific transcriptional regulatory programs responsible for the unique identity and function of each brain cell type have yet to be elucidated. Here, we probe the accessible chromatin in >800,000 individual nuclei from 45 regions spanning the adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei, and use the resulting data to define 491,818 candidate cis regulatory DNA elements in 160 distinct sub-types. We link a significant fraction of them to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators 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 non-coding risk variants associated with various neurological disease and traits in humans. To facilitate the dissemination of information, we have set up a web portal (http://catlas.org/mousebrain).

FMRP association with and regulation of Fragile X granules exhibit circuit-dependent requirements for the KH2 RNA binding domain

2018 ◽  
Author(s):  
Ellen C. Gingrich ◽  
Katherine A. Shepard ◽  
Molly E. Mitchell ◽  
Kirsty Sawicka ◽  
Jennifer C. Darnell ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Fragile X ◽  
Brain Regions ◽  
Binding Domain ◽  
Cell Type ◽  
Related Disorder ◽  
Rna Granules ◽  
Rna Binding Domain

AbstractThe localization and translation of mRNAs is controlled by a diverse array of ribonucleoprotein particles (RNPs), multimolecular complexes containing mRNAs and RNA binding proteins. Fragile X granules (FXGs) are a family of RNPs that exemplify the diversity of RNA granules in the mammalian nervous system. FXGs are found in a conserved subset of neurons, where they localize exclusively to the axonal compartment. Notably, the specific RNA binding proteins and mRNAs found in FXGs depend on brain circuit and neuron type, with all forebrain FXGs containing Fragile X mental retardation protein (FMRP), the protein mutated in the human autism-related disorder Fragile X syndrome. FMRP negatively regulates FXG abundance but is not required for their association with ribosomes or mRNA. To better understand the circuit-dependent mechanisms whereby FMRP associates with and regulates FXGs, we asked how a disease-causing point mutation, I304N, in the KH2 RNA binding domain of FMRP affects these granules in two brain regions – cortex and hippocampus. We found that FMRPI304N had a reduced association with FXGs, as it was absent from approximately half of FXGs in cortex and nearly all FXGs in hippocampus. FXG abundance correlated with the number of FMRP-containing FXGs, suggesting that FMRP regulates FXG abundance by KH2-independent mechanisms that occur locally within the granules. Together, these findings illustrate that cell type-dependent mechanisms guide the assembly of similar RNA granules. Further, point mutations in RNA granule components may lead to cell type-dependent phenotypes that produce atypical forms of disorders that normally arise from more severe mutations.

scholarly journals Shisa6 mediates cell-type specific regulation of depression in the nucleus accumbens

2021 ◽  
Author(s):  
Hee-Dae Kim ◽  
Jing Wei ◽  
Tanessa Call ◽  
Nicole Teru Quintus ◽  
Alexander J. Summers ◽  
...  
Keyword(s):  
Nucleus Accumbens ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Current Treatment ◽  
Specific Cell ◽  
Excitatory Synapses ◽  
Cell Type ◽  
Cell Type Specific ◽  
Specific Regulation ◽  
Circuit Function

AbstractDepression is the leading cause of disability and produces enormous health and economic burdens. Current treatment approaches for depression are largely ineffective and leave more than 50% of patients symptomatic, mainly because of non-selective and broad action of antidepressants. Thus, there is an urgent need to design and develop novel therapeutics to treat depression. Given the heterogeneity and complexity of the brain, identification of molecular mechanisms within specific cell-types responsible for producing depression-like behaviors will advance development of therapies. In the reward circuitry, the nucleus accumbens (NAc) is a key brain region of depression pathophysiology, possibly based on differential activity of D1- or D2- medium spiny neurons (MSNs). Here we report a circuit- and cell-type specific molecular target for depression, Shisa6, recently defined as an AMPAR component, which is increased only in D1-MSNs in the NAc of susceptible mice. Using the Ribotag approach, we dissected the transcriptional profile of D1- and D2-MSNs by RNA sequencing following a mouse model of depression, chronic social defeat stress (CSDS). Bioinformatic analyses identified cell-type specific genes that may contribute to the pathogenesis of depression, including Shisa6. We found selective optogenetic activation of the ventral tegmental area (VTA) to NAc circuit increases Shisa6 expression in D1-MSNs. Shisa6 is specifically located in excitatory synapses of D1-MSNs and increases excitability of neurons, which promotes anxiety- and depression-like behaviors in mice. Cell-type and circuit-specific action of Shisa6, which directly modulates excitatory synapses that convey aversive information, identifies the protein as a potential rapid-antidepressant target for aberrant circuit function in depression.

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