1
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Mews P, Van der Zee Y, Gurung A, Estill M, Futamura R, Kronman H, Ramakrishnan A, Ryan M, Reyes AA, Garcia BA, Browne CJ, Sidoli S, Shen L, Nestler EJ. Cell type-specific epigenetic priming of gene expression in nucleus accumbens by cocaine. SCIENCE ADVANCES 2024; 10:eado3514. [PMID: 39365860 PMCID: PMC11451531 DOI: 10.1126/sciadv.ado3514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 09/03/2024] [Indexed: 10/06/2024]
Abstract
A hallmark of addiction is the ability of drugs of abuse to trigger relapse after periods of prolonged abstinence. Here, we describe an epigenetic mechanism whereby chronic cocaine exposure causes lasting chromatin and downstream transcriptional modifications in the nucleus accumbens (NAc), a critical brain region controlling motivation. We link prolonged withdrawal from cocaine to the depletion of the histone variant H2A.Z, coupled with increased genome accessibility and latent priming of gene transcription, in D1 dopamine receptor-expressing medium spiny neurons (D1 MSNs) that relate to aberrant gene expression upon drug relapse. The histone chaperone ANP32E removes H2A.Z from chromatin, and we demonstrate that D1 MSN-selective Anp32e knockdown prevents cocaine-induced H2A.Z depletion and blocks cocaine's rewarding actions. By contrast, very different effects of cocaine exposure, withdrawal, and relapse were found for D2 MSNs. These findings establish histone variant exchange as an important mechanism and clinical target engaged by drugs of abuse to corrupt brain function and behavior.
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Affiliation(s)
- Philipp Mews
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yentl Van der Zee
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashik Gurung
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Molly Estill
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rita Futamura
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hope Kronman
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meagan Ryan
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Abner A. Reyes
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Caleb J. Browne
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medticine, New York, NY, USA
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric J. Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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2
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Krabbe S. Epigenetic control of memory formation. Science 2024; 385:367-368. [PMID: 39052819 DOI: 10.1126/science.adq8496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
A neuron's suitability to participate in a memory trace is modulated by its epigenetic state.
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Affiliation(s)
- Sabine Krabbe
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
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3
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Reda A, Hategan LA, McLean TAB, Creighton SD, Luo JQ, Chen SES, Hua S, Winston S, Reeves I, Padmanabhan A, Dahi TA, Ramzan F, Brimble MA, Murphy PJ, Walters BJ, Stefanelli G, Zovkic IB. Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification. Neuropsychopharmacology 2024; 49:1285-1295. [PMID: 38366138 PMCID: PMC11224360 DOI: 10.1038/s41386-024-01817-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Creating long-lasting memories requires learning-induced changes in gene expression, which are impacted by epigenetic modifications of DNA and associated histone proteins. Post-translational modifications (PTMs) of histones are key regulators of transcription, with different PTMs producing unique effects on gene activity and behavior. Although recent studies implicate histone variants as novel regulators of memory, effects of PTMs on the function of histone variants are rarely considered. We previously showed that the histone variant H2A.Z suppresses memory, but it is unclear if this role is impacted by H2A.Z acetylation, a PTM that is typically associated with positive effects on transcription and memory. To answer this question, we used a mutation approach to manipulate acetylation on H2A.Z without impacting acetylation of other histone types. Specifically, we used adeno-associated virus (AAV) constructs to overexpress mutated H2A.Z.1 isoforms that either mimic acetylation (acetyl-mimic) by replacing lysines 4, 7 and 11 with glutamine (KQ), or H2A.Z.1 with impaired acetylation (acetyl-defective) by replacing the same lysines with alanine (KA). Expressing the H2A.Z.1 acetyl-mimic (H2A.Z.1KQ) improved memory under weak learning conditions, whereas expressing the acetyl-defective H2A.Z.1KA generally impaired memory, indicating that the effect of H2A.Z.1 on memory depends on its acetylation status. RNA sequencing showed that H2A.Z.1KQ and H2A.Z.1KA uniquely impact the expression of different classes of genes in both females and males. Specifically, H2A.Z.1KA preferentially impacts genes involved in synaptic function, suggesting that acetyl-defective H2A.Z.1 impairs memory by altering synaptic regulation. Finally, we describe, for the first time, that H2A.Z is also involved in alternative splicing of neuronal genes, whereby H2A.Z depletion, as well as expression of H2A.Z.1 lysine mutants influence transcription and splicing of different gene targets, suggesting that H2A.Z.1 can impact behavior through effects on both splicing and gene expression. This is the first study to demonstrate that direct manipulation of H2A.Z post-translational modifications regulates memory, whereby acetylation adds another regulatory layer by which histone variants can fine tune higher brain functions through effects on gene expression and splicing.
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Affiliation(s)
- Anas Reda
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Luca A Hategan
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Timothy A B McLean
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Samantha D Creighton
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Jian Qi Luo
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Sean En Si Chen
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Shan Hua
- Departments of Biology and Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Stephen Winston
- Department of Surgery and Graduate school of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Isaiah Reeves
- Department of Surgery and Graduate school of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Aditya Padmanabhan
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Tarkan A Dahi
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Firyal Ramzan
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Mark A Brimble
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Patrick J Murphy
- Departments of Biology and Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Brandon J Walters
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Gilda Stefanelli
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.
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4
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Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.575103. [PMID: 38352334 PMCID: PMC10862743 DOI: 10.1101/2024.01.29.575103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Regulation of histone proteins affects gene expression through multiple mechanisms including exchange with histone variants. However, widely expressed variants of H2B remain elusive. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. We applied new tools including novel antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE, and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Lastly, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a novel mechanism linking histone variants to chromatin regulation, neuronal function, and memory. This work further identifies the first widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
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Affiliation(s)
- Emily R. Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine C. Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Anna J. Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Shreya D. Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Camille N. Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine T. Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Marc V. Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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5
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Stephens KE, Moore C, Vinson DA, White BE, Renfro Z, Zhou W, Ji Z, Ji H, Zhu H, Guan Y, Taverna SD. Identification of Regulatory Elements in Primary Sensory Neurons Involved in Trauma-Induced Neuropathic Pain. Mol Neurobiol 2024; 61:1845-1859. [PMID: 37792259 PMCID: PMC10896855 DOI: 10.1007/s12035-023-03673-5] [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: 07/06/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
Chronic pain is a significant public health issue that is often refractory to existing therapies. Here we use a multiomic approach to identify cis-regulatory elements that show differential chromatin accessibility and reveal transcription factor (TF) binding motifs with functional regulation in the rat dorsal root ganglion (DRG), which contain cell bodies of primary sensory neurons, after nerve injury. We integrated RNA-seq to understand how differential chromatin accessibility after nerve injury may influence gene expression. Using TF protein arrays and chromatin immunoprecipitation-qPCR, we confirmed C/EBPγ binding to a differentially accessible sequence and used RNA-seq to identify processes in which C/EBPγ plays an important role. Our findings offer insights into TF motifs that are associated with chronic pain. These data show how interactions between chromatin landscapes and TF expression patterns may work together to determine gene expression programs in rat DRG neurons after nerve injury.
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Affiliation(s)
- Kimberly E Stephens
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Arkansas Children's Research Institute, 13 Children's Way, Slot 512-47, Little Rock, AR, 72202, USA.
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.
| | - Cedric Moore
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
- , Present address: 20400 Century Blvd, Suite 120, Germantown, MD, USA
| | - David A Vinson
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA
| | - Bryan E White
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, 13 Children's Way, Slot 512-47, Little Rock, AR, 72202, USA
| | - Zachary Renfro
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, 13 Children's Way, Slot 512-47, Little Rock, AR, 72202, USA
- Present address: School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Weiqiang Zhou
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Zhicheng Ji
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Present address: Department of Biostatistics and Bioinformatics, School of Medicine, Duke University, Durham, NC, USA
| | - Hongkai Ji
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Yun Guan
- Department of Anesthesiology and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Neurological Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA.
- Center for Epigenetics, Johns Hopkins University, Baltimore, MD, USA.
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6
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Movahedi Motlagh F, Soleimanpour‐Lichaei HR, Shamsara M, Etemadzadeh A, Modarressi MH. CRISPR/Cas9 Ablated BCL11A Unveils the Genes with Possible Role of Globin Switching. Adv Pharm Bull 2023; 13:799-805. [PMID: 38022811 PMCID: PMC10676543 DOI: 10.34172/apb.2023.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 01/27/2023] [Accepted: 02/19/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Fetal hemoglobin (HbF) upregulation is a mitigating factor in β-hemoglobinopathies therapy like β-thalassemia and sickle cell diseases. Finding molecular mechanisms and the key regulators responsible for globin switching could be helpful to develop effective ways to HbF upregulation. In our prior in silico report, we identified a few factors that are likely to be responsible for globin switching. The goal of this study is to experimentally validate the factors. Methods We established K562 cell line with BCL11A knock down leading to increase in HBG1/2 using CRISPR/Cas9 system. Then, using quantitative polymerase chain reaction (qPCR), we determined the expression level of the factors which were previously identified in our prior in silico study. Results our analysis showed that BCL11A was substantially knocked down, resulting in the upregulation of HBG1/2 in the BCL11A-ablated K562 cells using CRISPR/Cas9 system. Additionally, the experimental data acquired in this study validated our prior bioinformatics findings about three potentially responsible genes for globin switching, namely HIST1H2Bl, TRIM58, and Al133243.2. Conclusion BCL11A is a promising candidate for the treatment of β-hemoglobinopathies, with high HbF reactivation. In addition, HIST1H2BL, TRIM58 and Al133243.2 are likely to be involved in the mechanism of hemoglobin switching. To further validate the selected genes, more experimental in vivo and in vitro studies are required.
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Affiliation(s)
| | - Hamid Reza Soleimanpour‐Lichaei
- Department of Stem Cells and Regenerative Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran, IR Iran
| | - Mehdi Shamsara
- Animal Biotechnology Group, Department of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Azadeh Etemadzadeh
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
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7
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Abstract
According to the commonly accepted opinion, memory engrams are formed and stored at the level of neural networks due to a change in the strength of synaptic connections between neurons. This hypothesis of synaptic plasticity (HSP), formulated by Donald Hebb in the 1940s, continues to dominate the directions of experimental studies and the interpretations of experimental results in the field. The universal acceptance of the HSP has transformed it from a hypothesis into an incontrovertible theory. In this article, I show that the entire body of experimental and clinical data obtained in studies of long-term memory in mammals and humans is inconsistent with the HSP. Instead, these data suggest that long-term memory is formed and stored at the intracellular level where it is reliably protected from ongoing synaptic activity, including pathological epileptic activity. It seems that the generally accepted HSP became a serious obstacle to understanding the mechanisms of memory and that progress in this field requires rethinking this doctrine and shifting experimental efforts toward exploring the intracellular mechanisms.
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Affiliation(s)
- Yuri I Arshavsky
- BioCircuits Institute, University of California San Diego, La Jolla, CA, USA
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8
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Richards BA, Kording KP. The study of plasticity has always been about gradients. J Physiol 2023; 601:3141-3149. [PMID: 37078235 DOI: 10.1113/jp282747] [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: 08/30/2022] [Accepted: 04/11/2023] [Indexed: 04/21/2023] Open
Abstract
The experimental study of learning and plasticity has always been driven by an implicit question: how can physiological changes be adaptive and improve performance? For example, in Hebbian plasticity only synapses from presynaptic neurons that were active are changed, avoiding useless changes. Similarly, in dopamine-gated learning synapse changes depend on reward or lack thereof and do not change when everything is predictable. Within machine learning we can make the question of which changes are adaptive concrete: performance improves when changes correlate with the gradient of an objective function quantifying performance. This result is general for any system that improves through small changes. As such, physiology has always implicitly been seeking mechanisms that allow the brain to approximate gradients. Coming from this perspective we review the existing literature on plasticity-related mechanisms, and we show how these mechanisms relate to gradient estimation. We argue that gradients are a unifying idea to explain the many facets of neuronal plasticity.
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Affiliation(s)
- Blake Aaron Richards
- Mila, Montreal, Quebec, Canada
- School of Computer Science, McGill University, Montreal, Quebec, Canada
- Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada
- Montreal Neurological Institute, Montreal, Quebec, Canada
- Learning in Machines and Brains Program, CIFAR, Toronto, Ontario, Canada
| | - Konrad Paul Kording
- Learning in Machines and Brains Program, CIFAR, Toronto, Ontario, Canada
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Neuroscience, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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9
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Guskjolen A, Cembrowski MS. Engram neurons: Encoding, consolidation, retrieval, and forgetting of memory. Mol Psychiatry 2023; 28:3207-3219. [PMID: 37369721 PMCID: PMC10618102 DOI: 10.1038/s41380-023-02137-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
Tremendous strides have been made in our understanding of the neurobiological substrates of memory - the so-called memory "engram". Here, we integrate recent progress in the engram field to illustrate how engram neurons transform across the "lifespan" of a memory - from initial memory encoding, to consolidation and retrieval, and ultimately to forgetting. To do so, we first describe how cell-intrinsic properties shape the initial emergence of the engram at memory encoding. Second, we highlight how these encoding neurons preferentially participate in synaptic- and systems-level consolidation of memory. Third, we describe how these changes during encoding and consolidation guide neural reactivation during retrieval, and facilitate memory recall. Fourth, we describe neurobiological mechanisms of forgetting, and how these mechanisms can counteract engram properties established during memory encoding, consolidation, and retrieval. Motivated by recent experimental results across these four sections, we conclude by proposing some conceptual extensions to the traditional view of the engram, including broadening the view of cell-type participation within engrams and across memory stages. In collection, our review synthesizes general principles of the engram across memory stages, and describes future avenues to further understand the dynamic engram.
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Affiliation(s)
- Axel Guskjolen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Mark S Cembrowski
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
- Department of Mathematics, University of British Columbia, Vancouver, BC, Canada.
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10
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Kelvington BA, Nickl-Jockschat T, Abel T. Neurobiological insights into twice-exceptionality: Circuits, cells, and molecules. Neurobiol Learn Mem 2022; 195:107684. [PMID: 36174887 PMCID: PMC9888516 DOI: 10.1016/j.nlm.2022.107684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 02/02/2023]
Abstract
Twice-exceptional learners face a unique set of challenges arising from the intersection of extraordinary talent and disability. Neurobiology research has the capacity to complement pedagogical research and provide support for twice-exceptional learners. Very few studies have attempted to specifically address the neurobiological underpinnings of twice-exceptionality. However, neurobiologists have built a broad base of knowledge in nervous system function spanning from the level of neural circuits to the molecular basis of behavior. It is known that distinct neural circuits mediate different neural functions, which suggests that 2e learning may result from enhancement in one circuit and disruption in another. Neural circuits are known to adapt and change in response to experience, a cellular process known as neuroplasticity. Plasticity is controlled by a bidirectional connection between the synapse, where neural signals are received, and the nucleus, where regulated gene expression can return to alter synaptic function. Complex molecular mechanisms compose this connection in distinct neural circuits, and genetic alterations in these mechanisms are associated with both memory enhancements and psychiatric disorder. Understanding the consequences of these changes at the molecular, cellular, and circuit levels will provide critical insights into the neurobiological bases of twice-exceptionality.
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Affiliation(s)
- Benjamin A Kelvington
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Thomas Nickl-Jockschat
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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11
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Li Y, Darabi R. Role of epigenetics in cellular reprogramming; from iPSCs to disease modeling and cell therapy. J Cell Biochem 2022; 123:147-154. [PMID: 34668236 PMCID: PMC8860854 DOI: 10.1002/jcb.30164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/03/2023]
Abstract
Epigenetics play a fundamental role in induced pluripotent stem cell (iPSC) technology due to their effect on iPSC's reprogramming efficiency and their subsequent role in iPSC differentiation toward a specific lineage. Epigenetics can skew the differentiation course of iPSCs toward a specific lineage based on the epigenetic memory of the source cells, or even lead to acquisition of new cell phenotypes, due to its aberrations during reprogramming. This viewpoint discusses key features of the epigenetic process during iPSC reprogramming/differentiation and outlines important epigenetic factors that need to be considered for successful generation and differentiation of iPSCs for downstream applications.
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Affiliation(s)
- Yong Li
- Department of Orthopaedic Surgery, BioMedical Engineering, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
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12
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Chang Y, Zhang J, Zhang J, Zhu W, Zheng Q, Qian Z, Wei C, Liu Y, Liu Z, Ren W, Han J. N6-methyladenosine RNA modification of glutamatergic neurons is associated with contextual fear discrimination. Physiol Behav 2022; 248:113741. [DOI: 10.1016/j.physbeh.2022.113741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 11/28/2022]
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13
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Stefanelli G, Makowski CE, Brimble MA, Hall M, Reda A, Creighton SD, Leonetti AM, McLean TAB, Zakaria JM, Baumbach J, Greer CB, Davidoff AM, Walters BJ, Murphy PJ, Zovkic IB. The histone chaperone Anp32e regulates memory formation, transcription, and dendritic morphology by regulating steady-state H2A.Z binding in neurons. Cell Rep 2021; 36:109551. [PMID: 34407406 PMCID: PMC8422973 DOI: 10.1016/j.celrep.2021.109551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 06/08/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Rapid removal of histone H2A.Z from neuronal chromatin is a key step in learning-induced gene expression and memory formation, but mechanisms underlying learning-induced H2A.Z removal are unclear. Anp32e was recently identified as an H2A.Z-specific histone chaperone that removes H2A.Z from nucleosomes in dividing cells, but its role in non-dividing neurons is unclear. Moreover, prior studies investigated Anp32e function under steady-state rather than stimulus-induced conditions. Here, we show that Anp32e regulates H2A.Z binding in neurons under steady-state conditions, with lesser impact on stimulus-induced H2A.Z removal. Functionally, Anp32e depletion leads to H2A.Z-dependent impairment in transcription and dendritic arborization in cultured hippocampal neurons, as well as impaired recall of contextual fear memory and transcriptional regulation. Together, these data indicate that Anp32e regulates behavioral and morphological outcomes by preventing H2A.Z accumulation in chromatin rather than by regulating activity-mediated H2A.Z dynamics.
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Affiliation(s)
- Gilda Stefanelli
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Claire E Makowski
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mark A Brimble
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Meaghan Hall
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Anas Reda
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Samantha D Creighton
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Amanda M Leonetti
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Timothy A B McLean
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Jacqueline M Zakaria
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Jennet Baumbach
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Celeste B Greer
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brandon J Walters
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA.
| | - Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada.
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14
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Gold AR, Glanzman DL. The central importance of nuclear mechanisms in the storage of memory. Biochem Biophys Res Commun 2021; 564:103-113. [PMID: 34020774 DOI: 10.1016/j.bbrc.2021.04.125] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022]
Abstract
The neurobiological nature of the memory trace (engram) remains controversial. The most widely accepted hypothesis at present is that long-term memory is stored as stable, learning-induced changes in synaptic connections. This hypothesis, the synaptic plasticity hypothesis of memory, is supported by extensive experimental data gathered from over 50 years of research. Nonetheless, there are important mnemonic phenomena that the synaptic plasticity hypothesis cannot, or cannot readily, account for. Furthermore, recent work indicates that epigenetic and genomic mechanisms play heretofore underappreciated roles in memory. Here, we critically assess the evidence that supports the synaptic plasticity hypothesis and discuss alternative non-synaptic, nuclear mechanisms of memory storage, including DNA methylation and retrotransposition. We argue that long-term encoding of memory is mediated by nuclear processes; synaptic plasticity, by contrast, represents a means of relatively temporary memory storage. In addition, we propose that memories are evaluated for their mnemonic significance during an initial period of synaptic storage; if assessed as sufficiently important, the memories then undergo nuclear encoding.
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Affiliation(s)
- Adam R Gold
- Behavioral Neuroscience Program, Department of Psychology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - David L Glanzman
- Department of Integrative Biology & Physiology, UCLA College, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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15
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Little DR, Lynch AM, Yan Y, Akiyama H, Kimura S, Chen J. Differential chromatin binding of the lung lineage transcription factor NKX2-1 resolves opposing murine alveolar cell fates in vivo. Nat Commun 2021; 12:2509. [PMID: 33947861 PMCID: PMC8096971 DOI: 10.1038/s41467-021-22817-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
Differential transcription of identical DNA sequences leads to distinct tissue lineages and then multiple cell types within a lineage, an epigenetic process central to progenitor and stem cell biology. The associated genome-wide changes, especially in native tissues, remain insufficiently understood, and are hereby addressed in the mouse lung, where the same lineage transcription factor NKX2-1 promotes the diametrically opposed alveolar type 1 (AT1) and AT2 cell fates. Here, we report that the cell-type-specific function of NKX2-1 is attributed to its differential chromatin binding that is acquired or retained during development in coordination with partner transcriptional factors. Loss of YAP/TAZ redirects NKX2-1 from its AT1-specific to AT2-specific binding sites, leading to transcriptionally exaggerated AT2 cells when deleted in progenitors or AT1-to-AT2 conversion when deleted after fate commitment. Nkx2-1 mutant AT1 and AT2 cells gain distinct chromatin accessible sites, including those specific to the opposite fate while adopting a gastrointestinal fate, suggesting an epigenetic plasticity unexpected from transcriptional changes. Our genomic analysis of single or purified cells, coupled with precision genetics, provides an epigenetic basis for alveolar cell fate and potential, and introduces an experimental benchmark for deciphering the in vivo function of lineage transcription factors.
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Affiliation(s)
- Danielle R Little
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Anne M Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yun Yan
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | | | - Shioko Kimura
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jichao Chen
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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16
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Mews P, Calipari ES, Day J, Lobo MK, Bredy T, Abel T. From Circuits to Chromatin: The Emerging Role of Epigenetics in Mental Health. J Neurosci 2021; 41:873-882. [PMID: 33446519 PMCID: PMC7880276 DOI: 10.1523/jneurosci.1649-20.2020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 02/01/2023] Open
Abstract
A central goal of neuroscience research is to understand how experiences modify brain circuits to guide future adaptive behavior. In response to environmental stimuli, neural circuit activity engages gene regulatory mechanisms within each cell. This activity-dependent gene expression is governed, in part, by epigenetic processes that can produce persistent changes in both neural circuits and the epigenome itself. The complex interplay between circuit activity and neuronal gene regulation is vital to learning and memory, and, when disrupted, is linked to debilitating psychiatric conditions, such as substance use disorder. To develop clinical treatments, it is paramount to advance our understanding of how neural circuits and the epigenome cooperate to produce behavioral adaptation. Here, we discuss how new genetic tools, used to manipulate neural circuits and chromatin, have enabled the discovery of epigenetic processes that bring about long-lasting changes in behavior relevant to mental health and disease.
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Affiliation(s)
- Philipp Mews
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10129
| | - Erin S Calipari
- Departments of Pharmacology, Molecular Physiology and Biophysics, Psychiatry and Behavioral Sciences; Vanderbilt Center for Addiction Research; Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37323
| | - Jeremy Day
- Department of Neurobiology, McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Mary Kay Lobo
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Timothy Bredy
- Queensland Brain Institute, University of Queensland, Brisbane, 4072, Australia
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242
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17
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Xu F, Li W, Yang X, Na L, Chen L, Liu G. The Roles of Epigenetics Regulation in Bone Metabolism and Osteoporosis. Front Cell Dev Biol 2021; 8:619301. [PMID: 33569383 PMCID: PMC7868402 DOI: 10.3389/fcell.2020.619301] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Osteoporosis is a metabolic disease characterized by decreased bone mineral density and the destruction of bone microstructure, which can lead to increased bone fragility and risk of fracture. In recent years, with the deepening of the research on the pathological mechanism of osteoporosis, the research on epigenetics has made significant progress. Epigenetics refers to changes in gene expression levels that are not caused by changes in gene sequences, mainly including DNA methylation, histone modification, and non-coding RNAs (lncRNA, microRNA, and circRNA). Epigenetics play mainly a post-transcriptional regulatory role and have important functions in the biological signal regulatory network. Studies have shown that epigenetic mechanisms are closely related to osteogenic differentiation, osteogenesis, bone remodeling and other bone metabolism-related processes. Abnormal epigenetic regulation can lead to a series of bone metabolism-related diseases, such as osteoporosis. Considering the important role of epigenetic mechanisms in the regulation of bone metabolism, we mainly review the research progress on epigenetic mechanisms (DNA methylation, histone modification, and non-coding RNAs) in the osteogenic differentiation and the pathogenesis of osteoporosis to provide a new direction for the treatment of bone metabolism-related diseases.
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Affiliation(s)
- Fei Xu
- College of Medical Technology, Shanghai University of Medicine and Health Sciences, Shanghai, China
- Collaborative Innovation Center, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Wenhui Li
- Collaborative Innovation Center, Shanghai University of Medicine and Health Sciences, Shanghai, China
- College of Clinical Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Xiao Yang
- Traditional Chinese Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lixin Na
- Collaborative Innovation Center, Shanghai University of Medicine and Health Sciences, Shanghai, China
- College of Public Health, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Linjun Chen
- College of Medical Technology, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Guobin Liu
- Traditional Chinese Vascular Surgery, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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