1
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Griffith EC, West AE, Greenberg ME. Neuronal enhancers fine-tune adaptive circuit plasticity. Neuron 2024; 112:3043-3057. [PMID: 39208805 DOI: 10.1016/j.neuron.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/22/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Neuronal activity-regulated gene expression plays a crucial role in sculpting neural circuits that underpin adaptive brain function. Transcriptional enhancers are now recognized as key components of gene regulation that orchestrate spatiotemporally precise patterns of gene transcription. We propose that the dynamics of enhancer activation uniquely position these genomic elements to finely tune activity-dependent cellular plasticity. Enhancer specificity and modularity can be exploited to gain selective genetic access to specific cell states, and the precise modulation of target gene expression within restricted cellular contexts enabled by targeted enhancer manipulation allows for fine-grained evaluation of gene function. Mounting evidence also suggests that enduring stimulus-induced changes in enhancer states can modify target gene activation upon restimulation, thereby contributing to a form of cell-wide metaplasticity. We advocate for focused exploration of activity-dependent enhancer function to gain new insight into the mechanisms underlying brain plasticity and cognitive dysfunction.
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Affiliation(s)
- Eric C Griffith
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Anne E West
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.
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2
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Kushinsky D, Tsivourakis E, Apelblat D, Roethler O, Breger-Mikulincer M, Cohen-Kashi Malina K, Spiegel I. Daily light-induced transcription in visual cortex neurons drives downward firing rate homeostasis and stabilizes sensory processing. Cell Rep 2024; 43:114701. [PMID: 39244753 DOI: 10.1016/j.celrep.2024.114701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/05/2024] [Accepted: 08/14/2024] [Indexed: 09/10/2024] Open
Abstract
Balancing plasticity and stability in neural circuits is essential for an animal's ability to learn from its environment while preserving proper processing and perception of sensory information. However, unlike the mechanisms that drive plasticity in neural circuits, the activity-induced molecular mechanisms that convey functional stability remain poorly understood. Focusing on the visual cortex of adult mice and combining transcriptomics, electrophysiology, and in vivo calcium imaging, we find that the daily appearance of light induces, in excitatory neurons, a large gene program along with rapid and transient increases in the ratio of excitation and inhibition (E/I ratio) and neural activity. Furthermore, we find that the light-induced transcription factor NPAS4 drives these daily normalizations of the E/I ratio and neural activity rates and that it stabilizes the neurons' response properties. These findings indicate that daily sensory-induced transcription normalizes the E/I ratio and drives downward firing rate homeostasis to maintain proper sensory processing and perception.
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Affiliation(s)
- Dahlia Kushinsky
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Emmanouil Tsivourakis
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Apelblat
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Roethler
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | | | - Katayun Cohen-Kashi Malina
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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3
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Zachariou M, Loizidou EM, Spyrou GM. Immediate-Early Genes as Influencers in Genetic Networks and their Role in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.586739. [PMID: 38585978 PMCID: PMC10996630 DOI: 10.1101/2024.03.29.586739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Immediate-early genes (IEGs) are a class of activity-regulated genes (ARGs) that are transiently and rapidly activated in the absence of de novo protein synthesis in response to neuronal activity. We explored the role of IEGs in genetic networks to pinpoint potential drug targets for Alzheimer's disease (AD). Using a combination of network analysis and genome-wide association study (GWAS) summary statistics we show that (1) IEGs exert greater topological influence across different human and mouse gene networks compared to other ARGs, (2) ARGs are sparsely involved in diseases and significantly more mutational constrained compared to non-ARGs, (3) Many AD-linked variants are in ARGs gene regions, mainly in MARK4 near FOSB, with an AD risk eQTL that increases MARK4 expression in cortical areas, (4) MARK4 holds an influential place in a dense AD multi-omic network and a high AD druggability score. Our work on IEGs' influential network role is a valuable contribution to guiding interventions for diseases marked by dysregulation of their downstream targets and highlights MARK4 as a promising underexplored AD-target.
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Affiliation(s)
| | - Eleni M Loizidou
- biobank.cy, Center of Excellence in Biobanking and Biomedical Research, University of Cyprus
| | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics
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4
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Roethler O, Zohar E, Cohen-Kashi Malina K, Bitan L, Gabel HW, Spiegel I. Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex. Neuron 2023; 111:2693-2708.e8. [PMID: 37354902 DOI: 10.1016/j.neuron.2023.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 03/29/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Experience-dependent plasticity of synapses modulates information processing in neural circuits and is essential for cognitive functions. The genome, via non-coding enhancers, was proposed to control information processing and circuit plasticity by regulating experience-induced transcription of genes that modulate specific sets of synapses. To test this idea, we analyze here the cellular and circuit functions of the genomic mechanisms that control the experience-induced transcription of Igf1 (insulin-like growth factor 1) in vasoactive intestinal peptide (VIP) interneurons (INs) in the visual cortex of adult mice. We find that two sensory-induced enhancers selectively and cooperatively drive the activity-induced transcription of Igf1 to thereby promote GABAergic inputs onto VIP INs and to homeostatically control the ratio between excitation and inhibition (E/I ratio)-in turn, this restricts neural activity in VIP INs and principal excitatory neurons and maintains spatial frequency tuning. Thus, enhancer-mediated activity-induced transcription maintains sensory processing in the adult cortex via homeostatic modulation of E/I ratio.
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Affiliation(s)
- Ori Roethler
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Zohar
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Katayun Cohen-Kashi Malina
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Lidor Bitan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Harrison Wren Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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5
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Nelson ED, Maynard KR, Nicholas KR, Tran MN, Divecha HR, Collado-Torres L, Hicks SC, Martinowich K. Activity-regulated gene expression across cell types of the mouse hippocampus. Hippocampus 2023; 33:1009-1027. [PMID: 37226416 PMCID: PMC11129873 DOI: 10.1002/hipo.23548] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/19/2023] [Accepted: 05/06/2023] [Indexed: 05/26/2023]
Abstract
Activity-regulated gene (ARG) expression patterns in the hippocampus (HPC) regulate synaptic plasticity, learning, and memory, and are linked to both risk and treatment responses for many neuropsychiatric disorders. The HPC contains discrete classes of neurons with specialized functions, but cell type-specific activity-regulated transcriptional programs are not well characterized. Here, we used single-nucleus RNA-sequencing (snRNA-seq) in a mouse model of acute electroconvulsive seizures (ECS) to identify cell type-specific molecular signatures associated with induced activity in HPC neurons. We used unsupervised clustering and a priori marker genes to computationally annotate 15,990 high-quality HPC neuronal nuclei from N = 4 mice across all major HPC subregions and neuron types. Activity-induced transcriptomic responses were divergent across neuron populations, with dentate granule cells being particularly responsive to activity. Differential expression analysis identified both upregulated and downregulated cell type-specific gene sets in neurons following ECS. Within these gene sets, we identified enrichment of pathways associated with varying biological processes such as synapse organization, cellular signaling, and transcriptional regulation. Finally, we used matrix factorization to reveal continuous gene expression patterns differentially associated with cell type, ECS, and biological processes. This work provides a rich resource for interrogating activity-regulated transcriptional responses in HPC neurons at single-nuclei resolution in the context of ECS, which can provide biological insight into the roles of defined neuronal subtypes in HPC function.
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Affiliation(s)
- Erik D. Nelson
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kristen R. Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kyndall R. Nicholas
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Matthew N Tran
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Heena R. Divecha
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, 21205
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6
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Harris N, Bates SG, Zhuang Z, Bernstein M, Stonemetz JM, Hill TJ, Yu YV, Calarco JA, Sengupta P. Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity. Curr Biol 2023; 33:1487-1501.e7. [PMID: 36977417 PMCID: PMC10133190 DOI: 10.1016/j.cub.2023.02.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/29/2023]
Abstract
Neurons modify their transcriptomes in response to an animal's experience. How specific experiences are transduced to modulate gene expression and precisely tune neuronal functions are not fully defined. Here, we describe the molecular profile of a thermosensory neuron pair in C. elegans experiencing different temperature stimuli. We find that distinct salient features of the temperature stimulus, including its duration, magnitude of change, and absolute value, are encoded in the gene expression program in this single neuron type, and we identify a novel transmembrane protein and a transcription factor whose specific transcriptional dynamics are essential to drive neuronal, behavioral, and developmental plasticity. Expression changes are driven by broadly expressed activity-dependent transcription factors and corresponding cis-regulatory elements that nevertheless direct neuron- and stimulus-specific gene expression programs. Our results indicate that coupling of defined stimulus characteristics to the gene regulatory logic in individual specialized neuron types can customize neuronal properties to drive precise behavioral adaptation.
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Affiliation(s)
- Nathan Harris
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
| | - Samuel G Bates
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Zihao Zhuang
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Matthew Bernstein
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Jamie M Stonemetz
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Tyler J Hill
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Yanxun V Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, Hubei Province, China
| | - John A Calarco
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, ON M5S 3G5, Canada
| | - Piali Sengupta
- Department of Biology, MS008, Brandeis University, 415 South Street, Waltham, MA 02454, USA.
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7
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Harris N, Bates S, Zhuang Z, Bernstein M, Stonemetz J, Hill T, Yu YV, Calarco JA, Sengupta P. Molecular encoding of stimulus features in a single sensory neuron type enables neuronal and behavioral plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525070. [PMID: 36711719 PMCID: PMC9882311 DOI: 10.1101/2023.01.22.525070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Neurons modify their transcriptomes in response to an animal’s experience. How specific experiences are transduced to modulate gene expression and precisely tune neuronal functions are not fully defined. Here, we describe the molecular profile of a thermosensory neuron pair in C. elegans experiencing different temperature stimuli. We find that distinct salient features of the temperature stimulus including its duration, magnitude of change, and absolute value are encoded in the gene expression program in this single neuron, and identify a novel transmembrane protein and a transcription factor whose specific transcriptional dynamics are essential to drive neuronal, behavioral, and developmental plasticity. Expression changes are driven by broadly expressed activity-dependent transcription factors and corresponding cis -regulatory elements that nevertheless direct neuron- and stimulus-specific gene expression programs. Our results indicate that coupling of defined stimulus characteristics to the gene regulatory logic in individual specialized neuron types can customize neuronal properties to drive precise behavioral adaptation.
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Affiliation(s)
- Nathan Harris
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Samuel Bates
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Zihao Zhuang
- Department of Biology, Brandeis University, Waltham, MA, USA
- Current address: Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | | | - Jamie Stonemetz
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Tyler Hill
- Department of Biology, Brandeis University, Waltham, MA, USA
| | - Yanxun V. Yu
- Department of Neurology, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - John A. Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA, USA
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8
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Pré D, Wooten AT, Biesmans S, Hinckley S, Zhou H, Sherman SP, Kakad P, Gearhart J, Bang AG. Development of a platform to investigate long-term potentiation in human iPSC-derived neuronal networks. Stem Cell Reports 2022; 17:2141-2155. [PMID: 35985330 PMCID: PMC9481914 DOI: 10.1016/j.stemcr.2022.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/25/2023] Open
Abstract
Impairment of long-term potentiation (LTP) is a common feature of many pre-clinical models of neurological disorders; however, studies in humans are limited by the inaccessibility of the brain. Human induced pluripotent stem cells (hiPSCs) provide a unique opportunity to study LTP in disease-specific genetic backgrounds. Here we describe a multi-electrode array (MEA)-based assay to investigate chemically induced LTP (cLTP) across entire networks of hiPSC-derived midbrain dopaminergic (DA) and cortical neuronal populations that lasts for days, allowing studies of the late phases of LTP and enabling detection of associated molecular changes. We show that cLTP on midbrain DA neuronal networks is largely independent of the N-methyl-D-aspartate receptor (NMDAR) and partially dependent on brain-derived neurotrophic factor (BDNF). Finally, we describe activity-regulated gene expression induced by cLTP. This cLTP-MEA assay platform will enable phenotype discovery and higher-throughput analyses of synaptic plasticity on hiPSC-derived neurons.
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Affiliation(s)
- Deborah Pré
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Alexander T Wooten
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Steven Biesmans
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sandy Hinckley
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Haowen Zhou
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sean P Sherman
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Priyanka Kakad
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeffrey Gearhart
- Henry M. Jackson Foundation for the Advancement of Military Medicine on Contract to USAF School of Aerospace Medicine, Wright-Patterson AFB, Dayton, OH 45433, USA
| | - Anne G Bang
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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9
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Apelblat D, Roethler O, Bitan L, Keren-Shaul H, Spiegel I. Meso-seq for in-depth transcriptomics in ultra-low amounts of FACS-purified neuronal nuclei. CELL REPORTS METHODS 2022; 2:100259. [PMID: 36046622 PMCID: PMC9421536 DOI: 10.1016/j.crmeth.2022.100259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/17/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022]
Abstract
Profiling of gene expression in sparse populations of genetically defined neurons is essential for dissecting the molecular mechanisms that control the development and plasticity of neural circuits. However, current transcriptomic approaches are ill suited for detailed mechanistic studies in sparse neuronal populations, as they either are technically complex and relatively expensive (e.g., single-cell RNA sequencing [RNA-seq]) or require large amounts of input material (e.g., traditional bulk RNA-seq). Thus, we established Meso-seq, a meso-scale protocol for identifying more than 10,000 robustly expressed genes in as little as 50 FACS-sorted neuronal nuclei. We demonstrate that Meso-seq works well for multiple neuroscience applications, including transcriptomics in antibody-labeled cortical neurons in mice and non-human primates, analyses of experience-regulated gene programs, and RNA-seq from visual cortex neurons labeled ultra-sparsely with viruses. Given its simplicity, robustness, and relatively low costs, Meso-seq is well suited for molecular-mechanistic studies in ultra-sparse neuronal populations in the brain.
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Affiliation(s)
- Daniella Apelblat
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Roethler
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Lidor Bitan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
- The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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10
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Pumo GM, Kitazawa T, Rijli FM. Epigenetic and Transcriptional Regulation of Spontaneous and Sensory Activity Dependent Programs During Neuronal Circuit Development. Front Neural Circuits 2022; 16:911023. [PMID: 35664458 PMCID: PMC9158562 DOI: 10.3389/fncir.2022.911023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Spontaneous activity generated before the onset of sensory transduction has a key role in wiring developing sensory circuits. From axonal targeting, to synapse formation and elimination, to the balanced integration of neurons into developing circuits, this type of activity is implicated in a variety of cellular processes. However, little is known about its molecular mechanisms of action, especially at the level of genome regulation. Conversely, sensory experience-dependent activity implements well-characterized transcriptional and epigenetic chromatin programs that underlie heterogeneous but specific genomic responses that shape both postnatal circuit development and neuroplasticity in the adult. In this review, we focus on our knowledge of the developmental processes regulated by spontaneous activity and the underlying transcriptional mechanisms. We also review novel findings on how chromatin regulates the specificity and developmental induction of the experience-dependent program, and speculate their relevance for our understanding of how spontaneous activity may act at the genomic level to instruct circuit assembly and prepare developing neurons for sensory-dependent connectivity refinement and processing.
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Affiliation(s)
- Gabriele M. Pumo
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
| | - Taro Kitazawa
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Filippo M. Rijli
- Laboratory of Neurodevelopmental Epigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department Biozentrum, University of Basel, Basel, Switzerland
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11
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Mishra P, Narayanan R. Stable continual learning through structured multiscale plasticity manifolds. Curr Opin Neurobiol 2021; 70:51-63. [PMID: 34416674 PMCID: PMC7611638 DOI: 10.1016/j.conb.2021.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
Biological plasticity is ubiquitous. How does the brain navigate this complex plasticity space, where any component can seemingly change, in adapting to an ever-changing environment? We build a systematic case that stable continuous learning is achieved by structured rules that enforce multiple, but not all, components to change together in specific directions. This rule-based low-dimensional plasticity manifold of permitted plasticity combinations emerges from cell type-specific molecular signaling and triggers cascading impacts that span multiple scales. These multiscale plasticity manifolds form the basis for behavioral learning and are dynamic entities that are altered by neuromodulation, metaplasticity, and pathology. We explore the strong links between heterogeneities, degeneracy, and plasticity manifolds and emphasize the need to incorporate plasticity manifolds into learning-theoretical frameworks and experimental designs.
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Affiliation(s)
- Poonam Mishra
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Rishikesh Narayanan
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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12
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Schiera G, Di Liegro CM, Di Liegro I. Involvement of Thyroid Hormones in Brain Development and Cancer. Cancers (Basel) 2021; 13:2693. [PMID: 34070729 PMCID: PMC8197921 DOI: 10.3390/cancers13112693] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/21/2022] Open
Abstract
The development and maturation of the mammalian brain are regulated by thyroid hormones (THs). Both hypothyroidism and hyperthyroidism cause serious anomalies in the organization and function of the nervous system. Most importantly, brain development is sensitive to TH supply well before the onset of the fetal thyroid function, and thus depends on the trans-placental transfer of maternal THs during pregnancy. Although the mechanism of action of THs mainly involves direct regulation of gene expression (genomic effects), mediated by nuclear receptors (THRs), it is now clear that THs can elicit cell responses also by binding to plasma membrane sites (non-genomic effects). Genomic and non-genomic effects of THs cooperate in modeling chromatin organization and function, thus controlling proliferation, maturation, and metabolism of the nervous system. However, the complex interplay of THs with their targets has also been suggested to impact cancer proliferation as well as metastatic processes. Herein, after discussing the general mechanisms of action of THs and their physiological effects on the nervous system, we will summarize a collection of data showing that thyroid hormone levels might influence cancer proliferation and invasion.
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Affiliation(s)
- Gabriella Schiera
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.S.); (C.M.D.L.)
| | - Carlo Maria Di Liegro
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche) (STEBICEF), University of Palermo, 90128 Palermo, Italy; (G.S.); (C.M.D.L.)
| | - Italia Di Liegro
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (Dipartimento di Biomedicina, Neuroscienze e Diagnostica avanzata) (Bi.N.D.), University of Palermo, 90127 Palermo, Italy
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Ryvkin J, Bentzur A, Shmueli A, Tannenbaum M, Shallom O, Dokarker S, Benichou JIC, Levi M, Shohat-Ophir G. Transcriptome Analysis of NPFR Neurons Reveals a Connection Between Proteome Diversity and Social Behavior. Front Behav Neurosci 2021; 15:628662. [PMID: 33867948 PMCID: PMC8044454 DOI: 10.3389/fnbeh.2021.628662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
Social behaviors are mediated by the activity of highly complex neuronal networks, the function of which is shaped by their transcriptomic and proteomic content. Contemporary advances in neurogenetics, genomics, and tools for automated behavior analysis make it possible to functionally connect the transcriptome profile of candidate neurons to their role in regulating behavior. In this study we used Drosophila melanogaster to explore the molecular signature of neurons expressing receptor for neuropeptide F (NPF), the fly homolog of neuropeptide Y (NPY). By comparing the transcription profile of NPFR neurons to those of nine other populations of neurons, we discovered that NPFR neurons exhibit a unique transcriptome, enriched with receptors for various neuropeptides and neuromodulators, as well as with genes known to regulate behavioral processes, such as learning and memory. By manipulating RNA editing and protein ubiquitination programs specifically in NPFR neurons, we demonstrate that the proper expression of their unique transcriptome and proteome is required to suppress male courtship and certain features of social group interaction. Our results highlight the importance of transcriptome and proteome diversity in the regulation of complex behaviors and pave the path for future dissection of the spatiotemporal regulation of genes within highly complex tissues, such as the brain.
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Affiliation(s)
- Julia Ryvkin
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Assa Bentzur
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Anat Shmueli
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Miriam Tannenbaum
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Omri Shallom
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Shiran Dokarker
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Jennifer I. C. Benichou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Mali Levi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Galit Shohat-Ophir
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
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14
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Mukherjee D, Gonzales BJ, Ashwal-Fluss R, Turm H, Groysman M, Citri A. Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in mice. eLife 2021; 10:65228. [PMID: 33724178 PMCID: PMC8057818 DOI: 10.7554/elife.65228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Drug addiction develops due to brain-wide plasticity within neuronal ensembles, mediated by dynamic gene expression. Though the most common approach to identify such ensembles relies on immediate early gene expression, little is known of how the activity of these genes is linked to modified behavior observed following repeated drug exposure. To address this gap, we present a broad-to-specific approach, beginning with a comprehensive investigation of brain-wide cocaine-driven gene expression, through the description of dynamic spatial patterns of gene induction in subregions of the striatum, and finally address functionality of region-specific gene induction in the development of cocaine preference. Our findings reveal differential cell-type specific dynamic transcriptional recruitment patterns within two subdomains of the dorsal striatum following repeated cocaine exposure. Furthermore, we demonstrate that induction of the IEG Egr2 in the ventrolateral striatum, as well as the cells within which it is expressed, are required for the development of cocaine seeking. The human brain is ever changing, constantly rewiring itself in response to new experiences, knowledge or information from the environment. Addictive drugs such as cocaine can hijack the genetic mechanisms responsible for this plasticity, creating dangerous, obsessive drug-seeking and consuming behaviors. Cocaine-induced plasticity is difficult to apprehend, however, as brain regions or even cell populations can react differently to the compound. For instance, sub-regions in the striatum – the brain area that responds to rewards and helps to plan movement – show distinct responses during progressive exposure to cocaine. And while researchers know that the drug immediately changes how neurons switch certain genes on and off, it is still unclear how these genetic modifications later affect behavior. Mukherjee, Gonzales et al. explored these questions at different scales, first focusing on how progressive cocaine exposure changed the way various gene programs were activated across the entire brain. This revealed that programs in the striatum were the most affected by the drug. Examining this region more closely showed that cocaine switches on genes in specific ‘spiny projection’ neuron populations, depending on where these cells are located and the drug history of the mouse. Finally, Mukherjee, Gonzales et al. used genetically modified mice to piece together cocaine exposure, genetic changes and modifications in behavior. These experiments revealed that the drive to seek cocaine depended on activation of the Egr2 gene in populations of spiny projection neurons in a specific sub-region of the striatum. The gene, which codes for a protein that regulates how genes are switched on and off, was itself strongly activated by cocaine intake. Cocaine addiction can have devastating consequences for individuals. Grasping how this drug alters the brain could pave the way for new treatments, while also providing information on the basic mechanisms underlying brain plasticity.
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Affiliation(s)
- Diptendu Mukherjee
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel.,Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ben Jerry Gonzales
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel.,Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reut Ashwal-Fluss
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
| | - Hagit Turm
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel.,Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maya Groysman
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel
| | - Ami Citri
- The Edmond and Lily Safra Center for Brain Sciences, Jerusalem, Israel.,Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Program in Child and Brain Development, Canadian Institute for Advanced Research, MaRS Centre, Toronto, Canada
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15
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Aponte-Santiago NA, Littleton JT. Synaptic Properties and Plasticity Mechanisms of Invertebrate Tonic and Phasic Neurons. Front Physiol 2020; 11:611982. [PMID: 33391026 PMCID: PMC7772194 DOI: 10.3389/fphys.2020.611982] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022] Open
Abstract
Defining neuronal cell types and their associated biophysical and synaptic diversity has become an important goal in neuroscience as a mechanism to create comprehensive brain cell atlases in the post-genomic age. Beyond broad classification such as neurotransmitter expression, interneuron vs. pyramidal, sensory or motor, the field is still in the early stages of understanding closely related cell types. In both vertebrate and invertebrate nervous systems, one well-described distinction related to firing characteristics and synaptic release properties are tonic and phasic neuronal subtypes. In vertebrates, these classes were defined based on sustained firing responses during stimulation (tonic) vs. transient responses that rapidly adapt (phasic). In crustaceans, the distinction expanded to include synaptic release properties, with tonic motoneurons displaying sustained firing and weaker synapses that undergo short-term facilitation to maintain muscle contraction and posture. In contrast, phasic motoneurons with stronger synapses showed rapid depression and were recruited for short bursts during fast locomotion. Tonic and phasic motoneurons with similarities to those in crustaceans have been characterized in Drosophila, allowing the genetic toolkit associated with this model to be used for dissecting the unique properties and plasticity mechanisms for these neuronal subtypes. This review outlines general properties of invertebrate tonic and phasic motoneurons and highlights recent advances that characterize distinct synaptic and plasticity pathways associated with two closely related glutamatergic neuronal cell types that drive invertebrate locomotion.
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Affiliation(s)
- Nicole A. Aponte-Santiago
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - J. Troy Littleton
- The Picower Institute for Learning and Memory, Department of Biology and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
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16
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Spiegel I. Experience-regulated molecular mechanisms in cortical GABAergic interneurons: from cellular functions to control over circuit plasticity. Curr Opin Neurobiol 2020; 67:145-154. [PMID: 33316573 DOI: 10.1016/j.conb.2020.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 01/30/2023]
Abstract
Experience-induced changes in GABAergic interneurons (INs) are thought to control the plasticity of neural circuits in the developing and adult cortex. However, it remains poorly understood how experience and the ensuing neuronal activity alter the properties and connectivity of specific IN subtypes and how these cellular changes, in turn, control the plasticity of cortical circuits. Here, I discuss recent experimental and theoretical studies that point to specific experience-induced changes in select IN subtypes as central regulators of plasticity in the cortex. In particular, I focus on the recent identification of several experience-regulated secreted molecules that modulate specific sets of synapses in IN subtypes. I argue that elucidating these molecular mechanisms will allow us to test experimentally the predictions made by theoretical models about the plasticity functions of specific IN subtypes.
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Affiliation(s)
- Ivo Spiegel
- Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel.
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17
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Regulation of Social Stress and Neural Degeneration by Activity-Regulated Genes and Epigenetic Mechanisms in Dopaminergic Neurons. Mol Neurobiol 2020; 57:4500-4510. [PMID: 32748368 PMCID: PMC7515954 DOI: 10.1007/s12035-020-02037-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/22/2020] [Indexed: 02/08/2023]
Abstract
Transcriptional and epigenetic regulation of both dopaminergic neurons and their accompanying glial cells is of great interest in the search for therapies for neurodegenerative disorders such as Parkinson’s disease (PD). In this review, we collate transcriptional and epigenetic changes identified in adult Drosophila melanogaster dopaminergic neurons in response to either prolonged social deprivation or social enrichment, and compare them with changes identified in mammalian dopaminergic neurons during normal development, stress, injury, and neurodegeneration. Surprisingly, a small set of activity-regulated genes (ARG) encoding transcription factors, and a specific pattern of epigenetic marks on gene promoters, are conserved in dopaminergic neurons over the long evolutionary period between mammals and insects. In addition to their classical function as immediate early genes to mark acute neuronal activity, these ARG transcription factors are repurposed in both insects and mammals to respond to chronic perturbations such as social enrichment, social stress, nerve injury, and neurodegeneration. We suggest that these ARG transcription factors and epigenetic marks may represent important targets for future therapeutic intervention strategies in various neurodegenerative disorders including PD.
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18
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Goodman JV, Yamada T, Yang Y, Kong L, Wu DY, Zhao G, Gabel HW, Bonni A. The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain. Nat Commun 2020; 11:3419. [PMID: 32647123 PMCID: PMC7347877 DOI: 10.1038/s41467-020-17065-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 06/05/2020] [Indexed: 12/13/2022] Open
Abstract
The development and function of the brain require tight control of gene expression. Genome architecture is thought to play a critical regulatory role in gene expression, but the mechanisms governing genome architecture in the brain in vivo remain poorly understood. Here, we report that conditional knockout of the chromatin remodeling enzyme Chd4 in granule neurons of the mouse cerebellum increases accessibility of gene regulatory sites genome-wide in vivo. Conditional knockout of Chd4 promotes recruitment of the architectural protein complex cohesin preferentially to gene enhancers in granule neurons in vivo. Importantly, in vivo profiling of genome architecture reveals that conditional knockout of Chd4 strengthens interactions among developmentally repressed contact domains as well as genomic loops in a manner that tightly correlates with increased accessibility, enhancer activity, and cohesin occupancy at these sites. Collectively, our findings define a role for chromatin remodeling in the control of genome architecture organization in the mammalian brain.
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Affiliation(s)
- Jared V Goodman
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, MO, USA
| | - Tomoko Yamada
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
- Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Yue Yang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Lingchun Kong
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Guoyan Zhao
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Azad Bonni
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA.
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19
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Tyssowski KM, Letai KC, Rendall SD, Tan C, Nizhnik A, Kaeser PS, Gray JM. Firing Rate Homeostasis Can Occur in the Absence of Neuronal Activity-Regulated Transcription. J Neurosci 2019; 39:9885-9899. [PMID: 31672790 PMCID: PMC6978944 DOI: 10.1523/jneurosci.1108-19.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/27/2019] [Accepted: 10/18/2019] [Indexed: 01/06/2023] Open
Abstract
Despite dynamic inputs, neuronal circuits maintain relatively stable firing rates over long periods. This maintenance of firing rate, or firing rate homeostasis, is likely mediated by homeostatic mechanisms such as synaptic scaling and regulation of intrinsic excitability. Because some of these homeostatic mechanisms depend on transcription of activity-regulated genes, including Arc and Homer1a, we hypothesized that activity-regulated transcription would be required for firing rate homeostasis. Surprisingly, however, we found that cultured mouse cortical neurons from both sexes grown on multi-electrode arrays homeostatically adapt their firing rates to persistent pharmacological stimulation even when activity-regulated transcription is disrupted. Specifically, we observed firing rate homeostasis in Arc knock-out neurons, as well as knock-out neurons lacking the activity-regulated transcription factors AP1 and SRF. Firing rate homeostasis also occurred normally during acute pharmacological blockade of transcription. Thus, firing rate homeostasis in response to increased neuronal activity can occur in the absence of neuronal-activity-regulated transcription.SIGNIFICANCE STATEMENT Neuronal circuits maintain relatively stable firing rates even in the face of dynamic circuit inputs. Understanding the molecular mechanisms that enable this firing rate homeostasis could potentially provide insight into neuronal diseases that present with an imbalance of excitation and inhibition. It has long been proposed that activity-regulated transcription could underlie firing rate homeostasis because activity-regulated genes turn on when neurons are above their target firing rates and include many genes that could regulate firing rate. Surprisingly, despite this prediction, we found that cortical neurons can undergo firing rate homeostasis in the absence of activity-regulated transcription, indicating that firing rate homeostasis can be controlled by non-transcriptional mechanisms.
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Affiliation(s)
| | | | | | - Chao Tan
- Neurobiology, Harvard Medical School, Boston, Massachusetts 02115
| | | | - Pascal S Kaeser
- Neurobiology, Harvard Medical School, Boston, Massachusetts 02115
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20
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Subregion-specific rules govern the distribution of neuronal immediate-early gene induction. Proc Natl Acad Sci U S A 2019; 117:23304-23310. [PMID: 31636216 DOI: 10.1073/pnas.1913658116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The induction of immediate-early gene (IEG) expression in brain nuclei in response to an experience is necessary for the formation of long-term memories. Additionally, the rapid dynamics of IEG induction and decay motivates the common use of IEG expression as markers for identification of neuronal assemblies ("ensembles") encoding recent experience. However, major gaps remain in understanding the rules governing the distribution of IEGs within neuronal assemblies. Thus, the extent of correlation between coexpressed IEGs, the cell specificity of IEG expression, and the spatial distribution of IEG expression have not been comprehensively studied. To address these gaps, we utilized quantitative multiplexed single-molecule fluorescence in situ hybridization (smFISH) and measured the expression of IEGs (Arc, Egr2, and Nr4a1) within spiny projection neurons (SPNs) in the dorsal striatum of mice following acute exposure to cocaine. Exploring the relevance of our observations to other brain structures and stimuli, we also analyzed data from a study of single-cell RNA sequencing of mouse cortical neurons. We found that while IEG expression is graded, the expression of multiple IEGs is tightly correlated at the level of individual neurons. Interestingly, we observed that region-specific rules govern the induction of IEGs in SPN subtypes within striatal subdomains. We further observed that IEG-expressing assemblies form spatially defined clusters within which the extent of IEG expression correlates with cluster size. Together, our results suggest the existence of IEG-expressing neuronal "superensembles," which are associated in spatial clusters and characterized by coherent and robust expression of multiple IEGs.
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21
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Pruunsild P, Bading H. Shaping the human brain: evolutionary cis-regulatory plasticity drives changes in synaptic activity-controlled adaptive gene expression. Curr Opin Neurobiol 2019; 59:34-40. [PMID: 31102862 DOI: 10.1016/j.conb.2019.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/10/2019] [Indexed: 01/09/2023]
Abstract
Neuronal activity-induced gene expression programs involved in synaptic structure- and plasticity-related functions are similar in mice and humans, yet bear distinct features. These include gains or losses of activity-responsiveness of certain genes and differences in gene induction profiles. Here, we discuss a possible origin of dissimilarities in activity-regulated transcription between species. We highlight that while synapse-to-nucleus signalling pathways are evolutionarily conserved, cis-regulatory plasticity has been driving species-specific remodelling of the activity-controlled enhancer landscape, thereby affecting gene regulation. In particular, evolutionary rearrangements of transcription factor binding site placements together with potential species-dependent developmental stage- and/or cell type-specific epigenetic and other trans-acting mechanisms are most likely at least in part accountable for between-species diversity in activity-regulated transcription. It is conceivable that cis-regulatory plasticity may have equipped the synaptic activity-driven adaptive gene program in human neurons with unique, species-specific qualities.
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Affiliation(s)
- Priit Pruunsild
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120 Heidelberg, Germany
| | - Hilmar Bading
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120 Heidelberg, Germany.
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