scholarly journals Whole-transcriptome RNA editing analysis in single cortical neurons links locus 15q11 with psychiatric illness

2019 ◽  
Author(s):  
Brendan Robert E. Ansell ◽  
Simon N. Thomas ◽  
Roberto Bonelli ◽  
Jacob E. Munro ◽  
Saskia Freytag ◽  
...  
Keyword(s):  
Rna Editing ◽  
Cortical Neurons ◽  
Serotonin Receptor ◽  
Target Genes ◽  
Linear Models ◽  
Inhibitory Neurons ◽  
Neuronal Nuclei ◽  
Neuropsychiatric Diseases ◽  
Excitatory Neurons ◽  
Cortical Regions

ABSTRACTBACKGROUNDConversion of adenosine to inosine in RNA by ADAR enzymes occurs at thousands of sites in the human transcriptome, and is essential for healthy brain development. This ‘RNA editing’ process is dysregulated in many neuropsychiatric diseases, but is little understood at the level of individual neurons.METHODSWe quantified RNA editing sites in full-length capture nuclear transcriptomes of 3055 neurons from six cortical regions of a neurotypical post-mortem female donor. Putative editing sites were intersected with sites in bulk human tissue transcriptomes including healthy and neuropsychiatric brain tissue, and sites identified in single nuclei from unrelated brain donors. Differential editing between cell types and cortical regions, and individual sites and genes therein, was quantified using linear models. Associations between gene expression and editing were also tested.RESULTSWe identified 41,930 RNA editing sites with robust read coverage in at least ten neuronal nuclei. Most sites were located within Alu repeats in introns or 3’ UTRs, and approximately 80% were catalogued in published RNA editing databases. We identified 9285 putative novel RNA editing sites, 29% of which were also detectable neuronal transcriptomes from unrelated donors. Inhibitory neurons showed higher overall transcriptome editing than excitatory neurons. Among the strongest correlates of global editing rates were snoRNAs from the SNORD115 and SNORD116 cluster (15q11), known to modulate serotonin receptor processing and to colocalize with ADAR2. We identified 29 genes preferentially edited in excitatory neurons and 44 genes edited more heavily in inhibitory neurons including RBFOX1, its target genes and small nucleolar RNA-associated genes in the autism-associated Prader-Willi locus 15q11. These results provide cell-type and spatial context for 1730 and 910 sites that are also edited in the brains of schizophrenic and autistic patients respectively, and a reference for future studies of RNA editing in single brain cells from these cohorts.CONCLUSIONSRNA editing, including thousands of previously unreported sites, is robustly detectable in single neuronal nuclei, where gene editing differences are stronger between cell subtypes than between cortical regions. Insufficient editing of ASD-related genes in inhibitory neurons may manifest in the specific perturbation of these cells in autism.

scholarly journals A survey of RNA editing at single cell resolution links interneurons to schizophrenia and autism

RNA ◽  
2021 ◽  
pp. rna.078804.121
Author(s):  
Brendan Robert E. Ansell ◽  
Simon N Thomas ◽  
Roberto Bonelli ◽  
Jacob E Munro ◽  
Saskia Freytag ◽  
...  
Keyword(s):  
Rna Editing ◽  
Rna Structure ◽  
Serotonin Receptor ◽  
Target Genes ◽  
Linear Models ◽  
Inhibitory Neurons ◽  
Neuronal Nuclei ◽  
Neuropsychiatric Diseases ◽  
Excitatory Neurons ◽  
Cortical Regions

BACKGROUND: Conversion of adenosine to inosine in RNA by ADAR enzymes occurs at thousands of sites in the human transcriptome, and is essential for healthy brain development. This editing process is dysregulated in many neuropsychiatric diseases, but has not yet been investigated at the level of individual neurons. METHODS: We quantified RNA editing sites in full-length capture nuclear transcriptomes of 3055 neurons from six cortical regions of a neurotypical post-mortem female donor. Putative editing sites were intersected with sites in bulk human tissue transcriptomes including healthy and neuropsychiatric brain tissue, and sites identified in single nuclei from unrelated brain donors. Differential editing between cell types and cortical regions, and individual sites and genes therein, was quantified using linear models. Associations between gene abundance and editing were also tested. RESULTS: We identified 41,930 RNA editing sites with robust read coverage in at least ten neuronal nuclei. Most sites were located within Alu repeats in introns or 3’ UTRs, and approximately 80% were catalogued in published RNA editing databases. We identified 9285 putative novel RNA editing sites, 29% of which were also detectable in neuronal transcriptomes from unrelated donors. Among the strongest correlates of global editing rates were snoRNAs from the SNORD115 and SNORD116 cluster (15q11), known to modulate serotonin receptor processing and to colocalize with ADAR2. Autism related genes were enriched with editing sites predicted to modify RNA structure. Inhibitory neurons showed higher overall transcriptome editing than excitatory neurons. Additionally, we identified 29 genes preferentially edited in excitatory neurons and 43 genes edited more heavily in inhibitory neurons including RBFOX1, its target genes, and small nucleolar RNA-associated genes in the autism-associated Prader-Willi locus 15q11. These results provide cell-type and spatial context for 1730 sites that are differentially edited in the brains of schizophrenic patients, and 910 sites in autistic patients. CONCLUSIONS: RNA editing, including thousands of previously unreported sites, is robustly detectable in single neuronal nuclei, where gene editing differences are stronger between cell subtypes than between cortical regions. Insufficient editing of autism-related genes in inhibitory neurons may manifest in the specific perturbation of these cells in autism.

scholarly journals A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

2018 ◽  
Vol 4 (9) ◽  
pp. eaau6190 ◽  
Author(s):  
Alexey Kozlenkov ◽  
Junhao Li ◽  
Pasha Apontes ◽  
Yasmin L. Hurd ◽  
William M. Byne ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Brain Cell ◽  
Inhibitory Neurons ◽  
Brain Diseases ◽  
Unique Role ◽  
Neuropsychiatric Diseases ◽  
Excitatory Neurons ◽  
Cell Type Specific

Brain function depends on interaction of diverse cell types whose gene expression and identity are defined, in part, by epigenetic mechanisms. Neuronal DNA contains two major epigenetic modifications, methylcytosine (mC) and hydroxymethylcytosine (hmC), yet their cell type–specific landscapes and relationship with gene expression are poorly understood. We report high-resolution (h)mC analyses, together with transcriptome and histone modification profiling, in three major cell types in human prefrontal cortex: glutamatergic excitatory neurons, medial ganglionic eminence–derived γ-aminobutyric acid (GABA)ergic inhibitory neurons, and oligodendrocytes. We detected a unique association between hmC and gene expression in inhibitory neurons that differed significantly from the pattern in excitatory neurons and oligodendrocytes. We also found that risk loci associated with neuropsychiatric diseases were enriched near regions of reduced hmC in excitatory neurons and reduced mC in inhibitory neurons. Our findings indicate differential roles for mC and hmC in regulation of gene expression in different brain cell types, with implications for the etiology of human brain diseases.

scholarly journals Synaptic Mechanisms for Bandwidth Tuning in Awake Mouse Primary Auditory Cortex

2018 ◽  
Vol 29 (7) ◽  
pp. 2998-3009 ◽  
Author(s):  
Haifu Li ◽  
Feixue Liang ◽  
Wen Zhong ◽  
Linqing Yan ◽  
Lucas Mesik ◽  
...  
Keyword(s):  
Auditory Cortex ◽  
Cortical Neurons ◽  
Primary Auditory Cortex ◽  
Cell Voltage ◽  
Inhibitory Neurons ◽  
Complex Sounds ◽  
Excitatory Neurons ◽  
Layer 4 ◽  
Bandwidth Tuning ◽  
Spatial Size

Abstract Spatial size tuning in the visual cortex has been considered as an important neuronal functional property for sensory perception. However, an analogous mechanism in the auditory system has remained controversial. In the present study, cell-attached recordings in the primary auditory cortex (A1) of awake mice revealed that excitatory neurons can be categorized into three types according to their bandwidth tuning profiles in response to band-passed noise (BPN) stimuli: nonmonotonic (NM), flat, and monotonic, with the latter two considered as non-tuned for bandwidth. The prevalence of bandwidth-tuned (i.e., NM) neurons increases significantly from layer 4 to layer 2/3. With sequential cell-attached and whole-cell voltage-clamp recordings from the same neurons, we found that the bandwidth preference of excitatory neurons is largely determined by the excitatory synaptic input they receive, and that the bandwidth selectivity is further enhanced by flatly tuned inhibition observed in all cells. The latter can be attributed at least partially to the flat tuning of parvalbumin inhibitory neurons. The tuning of auditory cortical neurons for bandwidth of BPN may contribute to the processing of complex sounds.

scholarly journals Somatosensory response properties of excitatory and inhibitory neurons in rat motor cortex

2011 ◽  
Vol 106 (3) ◽  
pp. 1355-1362 ◽  
Author(s):  
Peter D. Murray ◽  
Asaf Keller
Keyword(s):  
Motor Cortex ◽  
Receptive Field ◽  
Cortical Neurons ◽  
Inhibitory Neurons ◽  
Field Size ◽  
Spiking Neuron ◽  
Excitatory Neurons ◽  
Fast Spiking ◽  
Motor Cortical ◽  
Feedforward Inhibition

In sensory cortical networks, peripheral inputs differentially activate excitatory and inhibitory neurons. Inhibitory neurons typically have larger responses and broader receptive field tuning compared with excitatory neurons. These differences are thought to underlie the powerful feedforward inhibition that occurs in response to sensory input. In the motor cortex, as in the somatosensory cortex, cutaneous and proprioceptive somatosensory inputs, generated before and during movement, strongly and dynamically modulate the activity of motor neurons involved in a movement and ultimately shape cortical command. Human studies suggest that somatosensory inputs modulate motor cortical activity in a center excitation, surround inhibition manner such that input from the activated muscle excites motor cortical neurons that project to it, whereas somatosensory input from nearby, nonactivated muscles inhibit these neurons. A key prediction of this hypothesis is that inhibitory and excitatory motor cortical neurons respond differently to somatosensory inputs. We tested this prediction with the use of multisite extracellular recordings in anesthetized rats. We found that fast-spiking (presumably inhibitory) neurons respond to tactile and proprioceptive inputs at shorter latencies and larger response magnitudes compared with regular-spiking (presumably excitatory) neurons. In contrast, we found no differences in the receptive field size of these neuronal populations. Strikingly, all fast-spiking neuron pairs analyzed with cross-correlation analysis displayed common excitation, which was significantly more prevalent than common excitation for regular-spiking neuron pairs. These findings suggest that somatosensory inputs preferentially evoke feedforward inhibition in the motor cortex. We suggest that this provides a mechanism for dynamic selection of motor cortical modules during voluntary movements.

scholarly journals Cortical interneurons ensure maintenance of frequency tuning following adaptation

2017 ◽  
Author(s):  
Ryan G. Natan ◽  
Winnie Rao ◽  
Maria N. Geffen
Keyword(s):  
Frequency Response ◽  
Response Function ◽  
Cortical Neurons ◽  
Frequency Response Function ◽  
Frequency Tuning ◽  
Inhibitory Neurons ◽  
Sensory Stimuli ◽  
Cortical Interneurons ◽  
Excitatory Neurons ◽  
Shape Tuning

AbstractNeurons throughout the sensory pathway are tuned to specific aspects of stimuli. This selectivity is shaped by feedforward and recurrent excitatory-inhibitory interactions. In the auditory cortex (AC), two large classes of interneurons, parvalbumin- (PVs) and somatostatin- positive (SOMs) interneurons, differentially modulate frequency-dependent responses across the frequency response function of excitatory neurons. At the same time, the responsiveness of neurons in AC to sounds is dependent on the temporal context, with the majority of neurons exhibiting adaptation to repeated sounds. Here, we asked whether and how inhibitory neurons shape the frequency response function of excitatory neurons as a function of adaptation to temporal repetition of tones. The effects of suppressing both SOMs and PVs diverged for responses to preferred versus non-preferred frequencies following adaptation. Prior to adaptation, suppressing either SOM or PV inhibition drove both increases and decreases in spiking activity among cortical neurons. After adaptation, suppressing SOM activity caused predominantly disinhibitory effects, whereas suppressing PV activity still evoked bi-directional changes. SOM, but not PV-driven inhibition dynamically modulated frequency tuning as a function of adaptation. Additionally, testing across frequency tuning revealed that, unlike PVs, SOM-driven inhibition exhibited gain-like increases reflective of adaptation. Our findings suggest that distinct cortical interneurons differentially shape tuning to sensory stimuli across the neuronal receptive field, maintaining frequency selectivity of excitatory neurons during adaptation.

Electromagnetic radiation modulates synchronization in cortical neurons of Macaque brain

2019 ◽  
Vol 30 (08) ◽  
pp. 1950047
Author(s):  
Mary Vinaya ◽  
Rose P. Ignatius
Keyword(s):  
Electromagnetic Field ◽  
Cortical Neurons ◽  
Neural System ◽  
Inhibitory Neurons ◽  
Gamma Activity ◽  
Synaptic Coupling ◽  
Local Networks ◽  
High Gamma ◽  
Approximate Frequency ◽  
Cortical Regions

We study dynamical synchronization in a model of a neural system representing 47 cortical regions of Macaque brain under the effect of an electromagnetic field. This system is constituted by local networks of densely interconnected excitatory and inhibitory neurons. Coupling between the local networks is introduced through sparsely distributed excitatory connectivity. Voltage- and ligand-gated ion channels determine the neural dynamics of the networks. The effect of electromagnetic field on the neural system is studied by modulating magnetic flux on the membrane potential using memristor coupling. With the application of electromagnetic field and the modulation of long-range synaptic coupling, the system easily makes transition to synchronization. It is found that the threshold for synchrony between coupled local networks is lowered by the applied electromagnetic field. Also, electromagnetic field causes the neural subsystems to make low amplitude oscillations with an approximate frequency of 130 Hz. This indicates that electromagnetic field gives rise to high-gamma activity in the cortical regions of the brain which increases selective attention. This may facilitate adaptive brain function by giving rise to a rich collection of dynamics and contribute to the origin of complex patterns observed in the EEG.

scholarly journals Presynaptic GABAB Receptors Modulate Thalamic Excitation of Inhibitory and Excitatory Neurons in the Mouse Barrel Cortex

2004 ◽  
Vol 92 (5) ◽  
pp. 2762-2770 ◽  
Author(s):  
James T. Porter ◽  
Dalila Nieves
Keyword(s):  
Cortical Neurons ◽  
Barrel Cortex ◽  
Glutamate Release ◽  
Receptive Fields ◽  
Sensory Information ◽  
Gabab Receptors ◽  
Cortical Inhibition ◽  
Inhibitory Neurons ◽  
Excitatory Neurons

Cortical inhibition plays an important role in the processing of sensory information, and the enlargement of receptive fields by the in vivo application of GABAB receptor antagonists indicates that GABAB receptors mediate some of this cortical inhibition. Although there is evidence of postsynaptic GABAB receptors on cortical neurons, there is no evidence of GABAB receptors on thalamocortical terminals. Therefore to determine if presynaptic GABAB receptors modulate the thalamic excitation of layer IV inhibitory neurons and excitatory neurons in layers II–III and IV of the somatosensory “barrel” cortex of mice, we used a thalamocortical slice preparation and patch-clamp electrophysiology. Stimulation of the ventrobasal thalamus elicited excitatory postsynaptic currents (EPSCs) in cortical neurons. Bath application of baclofen, a selective GABAB receptor agonist, reversibly decreased AMPA receptor-mediated and N-methyl-d-aspartate (NMDA) receptor-mediated EPSCs in inhibitory and excitatory neurons. The GABAB receptor antagonist, CGP 35348, reversed the inhibition produced by baclofen. Blocking the postsynaptic GABAB receptor-mediated effects with a Cs+-based recording solution did not affect the inhibition, suggesting a presynaptic effect of baclofen. Baclofen reversibly increased the paired-pulse ratio and the coefficient of variation, consistent with the presynaptic inhibition of glutamate release. Our results indicate that the presynaptic activation of GABAB receptors modulates thalamocortical excitation of inhibitory and excitatory neurons and provide another mechanism by which cortical inhibition can modulate the processing of sensory information.

scholarly journals The Bacterial Enzyme Cas13 Interferes with Neurite Outgrowth from Cultured Cortical Neurons

Toxins ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 262
Author(s):  
Qin-Wei Wu ◽  
Josef P. Kapfhammer
Keyword(s):  
Rna Editing ◽  
Cortical Neurons ◽  
High Efficiency ◽  
Primary Cultures ◽  
Cultured Neurons ◽  
Therapeutic Tool ◽  
Bacterial Enzyme ◽  
Rna Targeting ◽  
Cultured Cortical Neurons ◽  
New Generation

The CRISPR-Cas13 system based on a bacterial enzyme has been explored as a powerful new method for RNA manipulation. Due to the high efficiency and specificity of RNA editing/interference achieved by this system, it is currently being developed as a new therapeutic tool for the treatment of neurological and other diseases. However, the safety of this new generation of RNA therapies is still unclear. In this study, we constructed a vector expressing CRISPR-Cas13 under a constitutive neuron-specific promoter. CRISPR-Cas13 from Leptotrichia wadei was expressed in primary cultures of mouse cortical neurons. We found that the presence of CRISPR-Cas13 impedes the development of cultured neurons. These results show a neurotoxic action of Cas13 and call for more studies to test for and possibly mitigate the toxic effects of Cas13 enzymes in order to improve CRISPR-Cas13-based tools for RNA targeting.

scholarly journals Role of Satb1 and Satb2 Transcription Factors in the Glutamate Receptors Expression and Ca2+ Signaling in the Cortical Neurons In Vitro

2021 ◽  
Vol 22 (11) ◽  
pp. 5968
Author(s):  
Egor A. Turovsky ◽  
Maria V. Turovskaya ◽  
Evgeniya I. Fedotova ◽  
Alexey A. Babaev ◽  
Viktor S. Tarabykin ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Nmda Receptor ◽  
Cortical Neurons ◽  
Target Genes ◽  
Cortical Cell ◽  
Inhibitory System ◽  
Selective Agonist ◽  
Genes Encoding ◽  
Deficient Mice

Transcription factors Satb1 and Satb2 are involved in the processes of cortex development and maturation of neurons. Alterations in the expression of their target genes can lead to neurodegenerative processes. Molecular and cellular mechanisms of regulation of neurotransmission by these transcription factors remain poorly understood. In this study, we have shown that transcription factors Satb1 and Satb2 participate in the regulation of genes encoding the NMDA-, AMPA-, and KA- receptor subunits and the inhibitory GABA(A) receptor. Deletion of gene for either Satb1 or Satb2 homologous factors induces the expression of genes encoding the NMDA receptor subunits, thereby leading to higher amplitudes of Ca2+-signals in neurons derived from the Satb1-deficient (Satb1fl/+ * NexCre/+) and Satb1-null mice (Satb1fl/fl * NexCre/+) in response to the selective agonist reducing the EC50 for the NMDA receptor. Simultaneously, there is an increase in the expression of the Gria2 gene, encoding the AMPA receptor subunit, thus decreasing the Ca2+-signals of neurons in response to the treatment with a selective agonist (5-Fluorowillardiine (FW)). The Satb1 deletion increases the sensitivity of the KA receptor to the agonist (domoic acid), in the cortical neurons of the Satb1-deficient mice but decreases it in the Satb1-null mice. At the same time, the Satb2 deletion decreases Ca2+-signals and the sensitivity of the KA receptor to the agonist in neurons from the Satb1-null and the Satb1-deficient mice. The Satb1 deletion affects the development of the inhibitory system of neurotransmission resulting in the suppression of the neuron maturation process and switching the GABAergic responses from excitatory to inhibitory, while the Satb2 deletion has a similar effect only in the Satb1-null mice. We show that the Satb1 and Satb2 transcription factors are involved in the regulation of the transmission of excitatory signals and inhibition of the neuronal network in the cortical cell culture.

scholarly journals Implications of Extended Inhibitory Neuron Development

2021 ◽  
Vol 22 (10) ◽  
pp. 5113
Author(s):  
Jae-Yeon Kim ◽  
Mercedes F. Paredes
Keyword(s):  
Neural Circuit ◽  
Inhibitory Neuron ◽  
Postnatal Period ◽  
Specific Pattern ◽  
Inhibitory Neurons ◽  
Gabaergic Interneuron ◽  
Gabaergic Interneurons ◽  
Neuron Development ◽  
Cortical Regions ◽  
Circuit Formation

A prolonged developmental timeline for GABA (γ-aminobutyric acid)-expressing inhibitory neurons (GABAergic interneurons) is an amplified trait in larger, gyrencephalic animals. In several species, the generation, migration, and maturation of interneurons take place over several months, in some cases persisting after birth. The late integration of GABAergic interneurons occurs in a region-specific pattern, especially during the early postnatal period. These changes can contribute to the formation of functional connectivity and plasticity, especially in the cortical regions responsible for higher cognitive tasks. In this review, we discuss GABAergic interneuron development in the late gestational and postnatal forebrain. We propose the protracted development of interneurons at each stage (neurogenesis, neuronal migration, and network integration), as a mechanism for increased complexity and cognitive flexibility in larger, gyrencephalic brains. This developmental feature of interneurons also provides an avenue for environmental influences to shape neural circuit formation.

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