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Bahabry R, Hauser RM, Sánchez RG, Jago SS, Ianov L, Stuckey RJ, Parrish RR, Ver Hoef L, Lubin FD. Alterations in DNA 5-hydroxymethylation patterns in the hippocampus of an experimental model of chronic epilepsy. Neurobiol Dis 2024:106638. [PMID: 39142613 DOI: 10.1016/j.nbd.2024.106638] [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: 10/17/2023] [Revised: 07/27/2024] [Accepted: 08/11/2024] [Indexed: 08/16/2024] Open
Abstract
Temporal lobe epilepsy (TLE) is a type of focal epilepsy characterized by spontaneous recurrent seizures originating from the hippocampus. The epigenetic reprogramming hypothesis of epileptogenesis suggests that the development of TLE is associated with alterations in gene transcription changes resulting in a hyperexcitable network in TLE. DNA 5-methylcytosine (5-mC) is an epigenetic mechanism that has been associated with chronic epilepsy. However, the contribution of 5-hydroxymethylcytosine (5-hmC), a product of 5-mC demethylation by the Ten-Eleven Translocation (TET) family proteins in chronic TLE is poorly understood. 5-hmC is abundant in the brain and acts as a stable epigenetic mark altering gene expression through several mechanisms. Here, we found that the levels of bulk DNA 5-hmC but not 5-mC were significantly reduced in the hippocampus of human TLE patients and in the kainic acid (KA) TLE rat model. Using 5-hmC hMeDIP-sequencing, we characterized 5-hmC distribution across the genome and found bidirectional regulation of 5-hmC at intergenic regions within gene bodies. We found that hypohydroxymethylated 5-hmC intergenic regions were associated with several epilepsy-related genes, including Gal, SV2, and Kcnj11 and hyperdroxymethylation 5-hmC intergenic regions were associated with Gad65, TLR4, and Bdnf gene expression. Mechanistically, Tet1 knockdown in the hippocampus was sufficient to decrease 5-hmC levels and increase seizure susceptibility following KA administration. In contrast, Tet1 overexpression in the hippocampus resulted in increased 5-hmC levels associated with improved seizure resiliency in response to KA. These findings suggest an important role for 5-hmC as an epigenetic regulator of epilepsy that can be manipulated to influence seizure outcomes.
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Affiliation(s)
- Rudhab Bahabry
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America.
| | - Rebecca M Hauser
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America.
| | - Richard G Sánchez
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America.
| | - Silvienne Sint Jago
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America.
| | - Lara Ianov
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States of America.
| | - Remy J Stuckey
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America.
| | - R Ryley Parrish
- Department of Cellular and Molecular Biology, Xenon Pharmaceuticals, Burnaby, BC, Canada
| | - Lawrence Ver Hoef
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, United States of America.
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States of America.
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Mitchnick KA, Marlatte H, Belchev Z, Gao F, Rosenbaum RS. Differential contributions of the hippocampal dentate gyrus and CA1 subfield to mnemonic discrimination. Hippocampus 2024; 34:278-283. [PMID: 38501294 DOI: 10.1002/hipo.23604] [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: 08/04/2023] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Evidence suggests that individual hippocampal subfields are preferentially involved in various memory-related processes. Here, we demonstrated dissociations in these memory processes in two unique individuals with near-selective bilateral damage within the hippocampus, affecting the dentate gyrus (DG) in case BL and the cornu ammonis 1 (CA1) subfield in case BR. BL was impaired in discriminating highly similar objects in memory (i.e., mnemonic discrimination) but exhibited preserved overall recognition of studied objects, regardless of similarity. Conversely, BR demonstrated impaired general recognition. These results provide evidence for the DG in discrimination processes, likely related to underlying pattern separation computations, and the CA1 in retention/retrieval.
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Affiliation(s)
- Krista A Mitchnick
- Department of Psychology, York University, Toronto, Ontario, Canada
- Rotman Research Institute at Baycrest Hospital, Toronto, Ontario, Canada
| | - Hannah Marlatte
- Rotman Research Institute at Baycrest Hospital, Toronto, Ontario, Canada
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Zorry Belchev
- Rotman Research Institute at Baycrest Hospital, Toronto, Ontario, Canada
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Fuqiang Gao
- Cognitive Neurology Research Group, Sunnybrook Hospital, Toronto, Ontario, Canada
| | - R Shayna Rosenbaum
- Department of Psychology, York University, Toronto, Ontario, Canada
- Rotman Research Institute at Baycrest Hospital, Toronto, Ontario, Canada
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3
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Tsang E, Han VX, Flutter C, Alshammery S, Keating BA, Williams T, Gloss BS, Graham ME, Aryamanesh N, Pang I, Wong M, Winlaw D, Cardamone M, Mohammad S, Gold W, Patel S, Dale RC. Ketogenic diet modifies ribosomal protein dysregulation in KMT2D Kabuki syndrome. EBioMedicine 2024; 104:105156. [PMID: 38768529 PMCID: PMC11134553 DOI: 10.1016/j.ebiom.2024.105156] [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: 01/10/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Kabuki syndrome (KS) is a genetic disorder caused by DNA mutations in KMT2D, a lysine methyltransferase that methylates histones and other proteins, and therefore modifies chromatin structure and subsequent gene expression. Ketones, derived from the ketogenic diet, are histone deacetylase inhibitors that can 'open' chromatin and encourage gene expression. Preclinical studies have shown that the ketogenic diet rescues hippocampal memory neurogenesis in mice with KS via the epigenetic effects of ketones. METHODS Single-cell RNA sequencing and mass spectrometry-based proteomics were used to explore molecular mechanisms of disease in individuals with KS (n = 4) versus controls (n = 4). FINDINGS Pathway enrichment analysis indicated that loss of function mutations in KMT2D are associated with ribosomal protein dysregulation at an RNA and protein level in individuals with KS (FDR <0.05). Cellular proteomics also identified immune dysregulation and increased abundance of other lysine modification and histone binding proteins, representing a potential compensatory mechanism. A 12-year-old boy with KS, suffering from recurrent episodes of cognitive decline, exhibited improved cognitive function and neuropsychological assessment performance after 12 months on the ketogenic diet, with concomitant improvement in transcriptomic ribosomal protein dysregulation. INTERPRETATION Our data reveals that lysine methyltransferase deficiency is associated with ribosomal protein dysfunction, with secondary immune dysregulation. Diet and the production of bioactive molecules such as ketone bodies serve as a significant environmental factor that can induce epigenetic changes and improve clinical outcomes. Integrating transcriptomic, proteomic, and clinical data can define mechanisms of disease and treatment effects in individuals with neurodevelopmental disorders. FUNDING This study was supported by the Dale NHMRC Investigator Grant (APP1193648) (R.D), Petre Foundation (R.D), and The Sydney Children's Hospital Foundation/Kids Research Early and Mid-Career Researcher Grant (E.T).
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Affiliation(s)
- Erica Tsang
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Velda X Han
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chloe Flutter
- The Kabuki Syndrome Foundation - Volunteer, Northbrook, IL, USA
| | - Sarah Alshammery
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Brooke A Keating
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Tracey Williams
- Kids Rehab, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Brian S Gloss
- Westmead Research Hub, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Mark E Graham
- Biomedical Proteomics, Children's Medical Research Institute, The University of Sydney, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, Westmead, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ignatius Pang
- Bioinformatics Group, Children's Medical Research Institute, Westmead, Sydney, NSW, Australia
| | - Melanie Wong
- The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - David Winlaw
- Heart Centre, Ann and Robert H. Lurie Children's Hospital of Chicago and Feinberg School of Medicine, Northwestern University, USA
| | - Michael Cardamone
- Sydney Children's Hospital, Randwick, NSW, Australia; School of Clinical Medicine, University of New South Wales, NSW, Australia
| | - Shekeeb Mohammad
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Wendy Gold
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW, Australia; Molecular Neurobiology Research Laboratory, Kids Research, The Children's Hospital at Westmead & the Children's Medical Research Institute, NSW, Australia
| | - Shrujna Patel
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Russell C Dale
- Kids Neuroscience Centre, The Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, NSW, Australia; The Children's Hospital at Westmead Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; The Brain and Mind Centre, The University of Sydney, Sydney, NSW, Australia.
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Pérez-Sisqués L, Bhatt SU, Matuleviciute R, Gileadi TE, Kramar E, Graham A, Garcia FG, Keiser A, Matheos DP, Cain JA, Pittman AM, Andreae LC, Fernandes C, Wood MA, Giese KP, Basson MA. The Intellectual Disability Risk Gene Kdm5b Regulates Long-Term Memory Consolidation in the Hippocampus. J Neurosci 2024; 44:e1544232024. [PMID: 38575342 PMCID: PMC11079963 DOI: 10.1523/jneurosci.1544-23.2024] [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: 02/18/2024] [Revised: 03/21/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024] Open
Abstract
The histone lysine demethylase KDM5B is implicated in recessive intellectual disability disorders, and heterozygous, protein-truncating variants in KDM5B are associated with reduced cognitive function in the population. The KDM5 family of lysine demethylases has developmental and homeostatic functions in the brain, some of which appear to be independent of lysine demethylase activity. To determine the functions of KDM5B in hippocampus-dependent learning and memory, we first studied male and female mice homozygous for a Kdm5b Δ ARID allele that lacks demethylase activity. Kdm5b Δ ARID/ Δ ARID mice exhibited hyperactivity and long-term memory deficits in hippocampus-dependent learning tasks. The expression of immediate early, activity-dependent genes was downregulated in these mice and hyperactivated upon a learning stimulus compared with wild-type (WT) mice. A number of other learning-associated genes were also significantly dysregulated in the Kdm5b Δ ARID/ Δ ARID hippocampus. Next, we knocked down Kdm5b specifically in the adult, WT mouse hippocampus with shRNA. Kdm5b knockdown resulted in spontaneous seizures, hyperactivity, and hippocampus-dependent long-term memory and long-term potentiation deficits. These findings identify KDM5B as a critical regulator of gene expression and synaptic plasticity in the adult hippocampus and suggest that at least some of the cognitive phenotypes associated with KDM5B gene variants are caused by direct effects on memory consolidation mechanisms.
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Affiliation(s)
- Leticia Pérez-Sisqués
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Shail U Bhatt
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Rugile Matuleviciute
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Talia E Gileadi
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Eniko Kramar
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - Andrew Graham
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Franklin G Garcia
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - Ashley Keiser
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - Dina P Matheos
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - James A Cain
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Alan M Pittman
- St. George's University of London, London SW17 0RE, United Kingdom
| | - Laura C Andreae
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Cathy Fernandes
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AB, United Kingdom
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - K Peter Giese
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, United Kingdom
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Hatherly Laboratories, Exeter EX4 4PS, United Kingdom
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5
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Navabpour S, Farrell K, Kincaid SE, Omar N, Musaus M, Lin Y, Xie H, Jarome TJ. Monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation. Learn Mem 2024; 31:a053912. [PMID: 38580378 PMCID: PMC11000578 DOI: 10.1101/lm.053912.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/07/2024] [Indexed: 04/07/2024]
Abstract
Posttranslational modification of histone proteins is critical for memory formation. Recently, we showed that monoubiquitination of histone H2B at lysine 120 (H2Bub) is critical for memory formation in the hippocampus. However, the transcriptome controlled by H2Bub remains unknown. Here, we found that fear conditioning in male rats increased or decreased the expression of 86 genes in the hippocampus but, surprisingly, siRNA-mediated knockdown of the H2Bub ligase, Rnf20, abolished changes in all but one of these genes. These findings suggest that monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation.
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Affiliation(s)
- Shaghayegh Navabpour
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Kayla Farrell
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Shannon E Kincaid
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Nour Omar
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Yu Lin
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia 24061, USA
| | - Hehuang Xie
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia 24061, USA
- Fralin Life Science Institute at Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Timothy J Jarome
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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6
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McCoy AM, Prevot TD, Mian MY, Sharmin D, Ahmad AN, Cook JM, Sibille EL, Lodge DJ. Extrasynaptic localization is essential for α5GABA A receptor modulation of dopamine system function. eNeuro 2024; 11:ENEURO.0344-23.2023. [PMID: 38413199 PMCID: PMC10972738 DOI: 10.1523/eneuro.0344-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 02/29/2024] Open
Abstract
Dopamine system dysfunction, observed in animal models with psychosis-like symptomatology, can be restored by targeting Gamma-Aminobutyric Acid type A receptors (GABAAR) containing the α5, but not α1, subunit in the ventral hippocampus (vHipp). The reason for this discrepancy in efficacy remains elusive; however, one key difference is that α1GABAARs are primarily located in the synapse, whereas α5GABAARs are mostly extrasynaptic. To test whether receptor location is responsible for this difference in efficacy, we injected a small interfering ribonucleic acid (siRNA) into the vHipp to knock down radixin, a scaffolding protein that holds α5GABAARs in the extrasynaptic space. We then administered GL-II-73, a positive allosteric modulator of α5GABAARs (α5-PAM) known to reverse shock-induced deficits in dopamine system function, to determine if shifting α5GABAARs from the extrasynaptic space to the synapse would prevent the effects of α5-PAM on dopamine system function. As expected, knockdown of radixin significantly decreased radixin-associated α5GABAARs and increased the proportion of synaptic α5GABAARs, without changing the overall expression of α5GABAARs. Importantly, GL-II-73 was no longer able to modulate dopamine neuron activity in radixin-knockdown rats, indicating that the extrasynaptic localization of α5GABAARs is critical for hippocampal modulation of the dopamine system. These results may have important implications for clinical use of GL-II-73, as periods of high hippocampal activity appear to favor synaptic α5GABAARs, thus efficacy may be diminished in conditions where aberrant hippocampal activity is present.Significance Statement Currently available treatments for psychosis, a debilitating symptom linked with several brain disorders, are inadequate. While they can help manage symptoms in some patients, they do so imperfectly. They are also associated with severe side effects that can cause discontinuation of medication. This study provides preclinical evidence that the drug, GL-II-73, possesses the ability to modulate dopamine activity, a key player in psychosis symptoms, and further provides some mechanistic details regarding these effects. Overall, this work contributes to the growing body of literature suggesting that GL-II-73 and similar compounds may possess antipsychotic efficacy.
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Affiliation(s)
- Alexandra M. McCoy
- Department of Pharmacology and Center for Biomedical Neuroscience, UT Health San Antonio, San Antonio, Texas 78229
- South Texas Veterans Health Care System, Audie L. Murphy Division, San Antonio, Texas 78229
| | - Thomas D. Prevot
- Campbell Family Mental Health Research Institute of CAMH, Toronto, Ontario M5G 2C1, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Md Yeunus Mian
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211
| | - Dishary Sharmin
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211
| | - Adeeba N. Ahmad
- University of Texas, Rio Grande Valley, Edinburg, Texas 78539
| | - James M. Cook
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211
| | - Etienne L. Sibille
- Campbell Family Mental Health Research Institute of CAMH, Toronto, Ontario M5G 2C1, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Daniel J. Lodge
- Department of Pharmacology and Center for Biomedical Neuroscience, UT Health San Antonio, San Antonio, Texas 78229
- South Texas Veterans Health Care System, Audie L. Murphy Division, San Antonio, Texas 78229
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McFadden T, Carucci I, Farrell K, Fletchall E, Jarome TJ. Hypothalamic DNA 5-hydroxymethylation levels are altered by diet-induced weight gain during the development of obesity in a sex-specific manner. Brain Res 2023; 1817:148478. [PMID: 37422205 PMCID: PMC10529936 DOI: 10.1016/j.brainres.2023.148478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023]
Abstract
Obesity is a major health concern that is associated with altered gene transcription in the hypothalamus. However, the mechanisms controlling this gene expression dysregulation remain largely unknown. DNA 5-hydroxymethylation (5-hmC) is a potent transcriptional activator that is expressed at 10 times higher levels in the brain than the periphery. Despite this, no study has examined if DNA 5-hmC is altered in the brain following exposure to obesogenic diets or contributes to abnormal weight gain over time. Here, we used a rodent diet-induced obesity model in combination with quantitative molecular assays and CRISPR-dCas9 manipulations to test the role of hypothalamic DNA 5-hmC in abnormal weight gain in male and female rats. We found that males, but not females, have decreased levels of DNA 5-hmC in the hypothalamus following exposure to a high fat diet, which directly correlate with increased body weight. Short-term exposure to a high fat diet, which does not result in significant weight gain, resulted in decreased hypothalamic DNA 5-hmC levels, suggesting these changes occur prior to obesity development. Moreover, decreases in DNA 5-hmC persist even after the high fat diet is removed, though the extent of this is diet-dependent. Importantly, CRISPR-dCas9-mediated upregulation of DNA 5-hmC enzymes in the male, but not female, ventromedial nucleus of the hypothalamus significantly reduced the percentage of weight gained on the high fat diet relative to controls. These results suggest that hypothalamic DNA 5-hmC is an important sex-specific regulator of abnormal weight gain following exposure to high fat diets.
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Affiliation(s)
| | - Isabella Carucci
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | | | - Timothy J Jarome
- School of Animal Sciences, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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8
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Bahabry R, Hauser RM, Sánchez RG, Jago SS, Ianov L, Stuckey RJ, Parrish RR, Hoef LV, Lubin FD. Alterations in DNA 5-hydroxymethylation Patterns in the Hippocampus of an Experimental Model of Refractory Epilepsy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560698. [PMID: 37873276 PMCID: PMC10592907 DOI: 10.1101/2023.10.03.560698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Temporal lobe epilepsy (TLE) is a type of focal epilepsy characterized by spontaneous recurrent seizures originating from the hippocampus. The epigenetic reprogramming hypothesis of epileptogenesis suggests that the development of TLE is associated with alterations in gene transcription changes resulting in a hyperexcitable network in TLE. DNA 5-methylcytosine (5-mC) is an epigenetic mechanism that has been associated with chronic epilepsy. However, the contribution of 5-hydroxymethylcytosine (5-hmC), a product of 5-mC demethylation by the Ten-Eleven Translocation (TET) family proteins in chronic TLE is poorly understood. 5-hmC is abundant in the brain and acts as a stable epigenetic mark altering gene expression through several mechanisms. Here, we found that the levels of bulk DNA 5-hmC but not 5-mC were significantly reduced in the hippocampus of human TLE patients and in the kainic acid (KA) TLE rat model. Using 5-hmC hMeDIP-sequencing, we characterized 5-hmC distribution across the genome and found bidirectional regulation of 5-hmC at intergenic regions within gene bodies. We found that hypohydroxymethylated 5-hmC intergenic regions were associated with several epilepsy-related genes, including Gal , SV2, and Kcnj11 and hyperdroxymethylation 5-hmC intergenic regions were associated with Gad65 , TLR4 , and Bdnf gene expression. Mechanistically, Tet1 knockdown in the hippocampus was sufficient to decrease 5-hmC levels and increase seizure susceptibility following KA administration. In contrast, Tet1 overexpression in the hippocampus resulted in increased 5-hmC levels associated with improved seizure resiliency in response to KA. These findings suggest an important role for 5-hmC as an epigenetic regulator of epilepsy that can be manipulated to influence seizure outcomes.
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9
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McCoy AM, Prevot TD, Mian MY, Sharmin D, Ahmad AN, Cook JM, Sibille EL, Lodge DJ. Extrasynaptic localization is essential for α5GABA A receptor modulation of dopamine system function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548744. [PMID: 37502875 PMCID: PMC10370028 DOI: 10.1101/2023.07.12.548744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Dopamine system dysfunction, observed in animal models with psychosis-like symptomatology, can be restored by targeting Gamma-Aminobutyric Acid type A receptors (GABA A R) containing the α5, but not α1, subunit in the ventral hippocampus (vHipp). The reason for this discrepancy in efficacy remains elusive; however, one key difference is that α1GABA A Rs are primarily located in the synapse, whereas α5GABA A Rs are mostly extrasynaptic. To test whether receptor location is responsible for this difference in efficacy, we injected a small interfering ribonucleic acid (siRNA) into the vHipp to knock down radixin, a scaffolding protein that holds α5GABA A Rs in the extrasynaptic space. We then administered GL-II-73, a positive allosteric modulator of α5GABA A Rs (α5-PAM) known to reverse shock-induced deficits in dopamine system function, to determine if shifting α5GABA A Rs from the extrasynaptic space to the synapse would prevent the effects of α5-PAM on dopamine system function. As expected, knockdown of radixin significantly decreased radixin-associated α5GABA A Rs and increased the proportion of synaptic α5GABA A Rs, without changing the overall expression of α5GABA A Rs. Importantly, GL-II-73 was no longer able to modulate dopamine neuron activity in radixin-knockdown rats, indicating that the extrasynaptic localization of α5GABA A Rs is critical for hippocampal modulation of the dopamine system. These results may have important implications for clinical use of GL-II-73, as periods of high hippocampal activity appear to favor synaptic α5GABA A Rs, thus efficacy may be diminished in conditions where aberrant hippocampal activity is present. Significance Statement Dopamine activity is known to be altered in both psychosis patients and in animal models, with promising new antipsychotics restoring normal dopamine system function. One such drug is GL-II-73, a positive allosteric modulator of α5GABA A Rs (α5-PAM). Interestingly, previous research has shown that a positive allosteric modulator of α1GABA A Rs (α1-PAM) does not share this ability, even when directly given to the ventral hippocampus, a region known to modulate dopamine activity. One potential explanation for this difference we examined in this study is that α1GABA A Rs are primarily located in the synapse, whereas α5GABA A Rs are mostly extrasynaptic. Determining the mechanism of this differential efficacy could lead to the refinement of antipsychotic treatment and improve patient outcomes overall.
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Yang Z, Jia Y, Wang S, Zhang Y, Fan W, Wang X, He L, Shen X, Yang X, Zhang Y, Yang H. Retinoblastoma-Binding Protein 5 Regulates H3K4 Methylation Modification to Inhibit the Proliferation of Melanoma Cells by Inactivating the Wnt/ β-Catenin and Epithelial-Mesenchymal Transition Pathways. JOURNAL OF ONCOLOGY 2023; 2023:5093941. [PMID: 36866240 PMCID: PMC9974310 DOI: 10.1155/2023/5093941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/29/2022] [Accepted: 01/20/2023] [Indexed: 02/25/2023]
Abstract
Histone 3 lysine 4 methylation (H3K4me), especially histone 3 lysine 4 trimethylation (H3K4me3), is one of the most extensively studied patterns of histone modification and plays crucial roles in many biological processes. However, as a part of H3K4 methyltransferase that participates in H3K4 methylation and transcriptional regulation, retinoblastoma-binding protein 5 (RBBP5) has not been well studied in melanoma. The present study sought to explore RBBP5-mediated H3K4 histone modification and the potential mechanisms in melanoma. RBBP5 expression in melanoma and nevi specimens was detected by immunohistochemistry. Western blotting was performed for three pairs of melanoma cancer tissues and nevi tissues. In vitro and in vivo assays were used to investigate the function of RBBP5. The molecular mechanism was determined using RT-qPCR, western blotting, ChIP assays, and Co-IP assays. Our study showed that RBBP5 was significantly downregulated in melanoma tissue and cells compared with nevi tissues and normal epithelia cells (P < 0.05). Reducing RBBP5 in human melanoma cells leads to H3K4me3 downregulation and promotes cell proliferation, migration, and invasion. On the one hand, we verified that WSB2 was an upstream gene of RBBP5-mediated H3K4 modification, which could directly bind to RBBP5 and negatively regulate its expression. On the other hand, we also confirmed that p16 (a cancer suppressor gene) was a downstream target of H3K4me3, the promoter of which can directly bind to H3K4me3. Mechanistically, our data revealed that RBBP5 inactivated the Wnt/β-catenin and epithelial-mesenchymal transition (EMT) pathways (P < 0.05), leading to melanoma suppression. Histone methylation is rising as an important factor affecting tumorigenicity and tumor progression. Our findings verified the significance of RBBP5-mediated H3K4 modification in melanoma and the potential regulatory mechanisms of melanoma proliferation and growth, suggesting that RBBP5 is a potential therapeutic target for the treatment of melanoma.
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Affiliation(s)
- Zhiqin Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
- 2Departments of Gynecology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Yue Jia
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Shaojia Wang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Yongjun Zhang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Wen Fan
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
- 3Departments of Reproduction, The Second Affiliated Hospital of Kunming Medical University, Kunming 650106, China
| | - Xin Wang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Liang He
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Xiaoyu Shen
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Xiangqun Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Yi Zhang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
| | - Hongying Yang
- 1Department of Gynecology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming 650118, China
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11
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Comparative Study of the Effect of a DNA Methyltransferase Inhibitor and a Histone Deacetylase Inhibitor on Memory Formation Processes in Anterograde Amnesia. Bull Exp Biol Med 2022; 174:1-6. [PMID: 36437324 DOI: 10.1007/s10517-022-05636-7] [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: 04/15/2022] [Indexed: 11/29/2022]
Abstract
The participation of DNA methylation and histone acetylation in the mechanisms of anterograde amnesia and memory recovery was studied on grape snails trained in conditioned food aversion. Anterograde amnesia developed 10 days after memory reconsolidation impairment with an NMDA glutamate receptor antagonist and was characterized by long-term memory formation impairment upon repeated training. DNA methyltransferase inhibitor injections to snails 1 h before repeated training, as well as 15 min or 4 h after repeated training, caused rapid formation of memory that persisted for at least 10 days. Injections of histone deacetylase inhibitor before repeated training also induced the formation of a stable long-term memory. However, administration of histone deacetylase inhibitor 15 min after repeated training initiated a temporary memory recovery. Injections of the inhibitor 4 h after repeated training were ineffective. These results indicate that histone-dependent chromatin remodeling and DNA methylation are selectively involved in the mechanisms of anterograde amnesia and memory recovery.
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Fernandes V, Preeti K, Sood A, Nair KP, Khan S, Rao BSS, Khatri DK, Singh SB. Neuroepigenetic Changes in DNA Methylation Affecting Diabetes-Induced Cognitive Impairment. Cell Mol Neurobiol 2022:10.1007/s10571-022-01278-5. [PMID: 36138280 DOI: 10.1007/s10571-022-01278-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
Chronic diabetic conditions have been associated with certain cerebral complications, that include neurobehavioral dysfunctional patterns and morphological alterations of neurons, especially the hippocampus. Neuroanatomical studies done by the authors have shown decreased total dendritic length, intersections, dendritic length per branch order and nodes in the CA1 hippocampal region of the diabetic brain as compared to its normal control group, indicating reduced dendritic arborization of the hippocampal CA1 neurons. Epigenetic alterations in the brain are well known to affect age-associated disorders, however its association with the evolving diabetes-induced damage in the brain is still not fully understood. DNA hypermethylation within the neurons, tend to silent the gene expression of several regulatory proteins. The findings in the study have shown an increase in global DNA methylation in palmitic acid-induced lipotoxic Neuro-2a cells as well as within the diabetic mice brain. Inhibiting DNA methylation, restored the levels of HSF1 and certain HSPs, suggesting plausible effect of DNMTs in maintaining the proteostasis and synaptic fidelity. Neuroinflammation, as exhibited by the astrocyte activation (GFAP), were further significantly decreased in the 5-azadeoxycytidine group (DNMT inhibitor). This was further evidenced by decrease in proinflammatory cytokines TNF⍺, IL-6, and mediators iNOS and Phospho-NFkB. Our results suggest that changes in DNA methylation advocate epigenetic dysregulation and its involvement in disrupting the synaptic exactitude in the hippocampus of diabetic mice model, providing an insight into the pathophysiology of diabetes-induced neuroepigenetic changes.
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Affiliation(s)
- Valencia Fernandes
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Kumari Preeti
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Anika Sood
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Kala P Nair
- Department of Neurophysiology, National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru, Karnataka, 560029, India
| | - Sabiya Khan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - B S Shankaranarayana Rao
- Department of Neurophysiology, National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru, Karnataka, 560029, India
| | - Dharmendra Kumar Khatri
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
| | - Shashi Bala Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
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13
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Zhang D, Zhou Y, Huang R, Zhai Y, Wu D, An X, Zhang S, Shi L, Li Q, Kong X, Yu H, Li Z. LncRNA affects epigenetic reprogramming of porcine embryo development by regulating global epigenetic modification and the downstream gene SIN3A. Front Physiol 2022; 13:971965. [PMID: 36187791 PMCID: PMC9523245 DOI: 10.3389/fphys.2022.971965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
The study of preimplantation development is of great significance to reproductive biology and regenerative medicine. With the development of high-throughput deep sequencing technology, it has been found that lncRNAs play a very important role in the regulation of embryonic development. In this study, key lncRNAs that regulate embryonic development were screened by analyzing the expression pattern of lncRNAs in porcine in vivo fertilization (IVV) embryos. By knocking down lncRNA expression in in vitro fertilization (IVF) embryos, we investigated its function and mechanism of regulating embryonic development. The results showed that the expression pattern of lncRNA was consistent with the time of gene activation. The lncRNAs were highly expressed in the 4-cell to blastocyst stage but barely expressed in the oocytes and 2-cell stage. So we speculated this part of lncRNAs may regulate gene expression. The lncRNA LOC102165808 (named lncT because the gene near this lncRNA is TFAP2C) was one of them. The knockdown (KD) of lncT inhibited embryonic development, resulting in decreased H3K4me3, H3K4me2, and H3K9me3, and increased DNA methylation. Meanwhile, RNAseq showed SIN3A was the top decreased gene in lncT-KD embryos. There was a severe blastocyst formation defect in SIN3A-KD embryos. Both lncT and SIN3A could affect NANOG and induce more cell apoptosis. In conclusion, the knockdown of lncT inhibits embryonic development by regulating H3K4me3, H3K4me2, DNA methylation, pluripotency gene, and apoptosis, and SIN3A is one of the downstream genes of lncT in regulating embryonic development.
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Affiliation(s)
- Daoyu Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Yongfeng Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Rong Huang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Yanhui Zhai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Di Wu
- Department of Emergency Medicine, First Hospital, Jilin University, Changchun, China
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Lijing Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Xiangjie Kong
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun, China
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
- *Correspondence: Ziyi Li,
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14
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Farrell K, Auerbach A, Musaus M, Jarome TJ. The epigenetic role of proteasome subunit RPT6 during memory formation in female rats. Learn Mem 2022; 29:256-264. [PMID: 36206393 PMCID: PMC9488026 DOI: 10.1101/lm.053498.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022]
Abstract
Reports of sex differences in the neurobiology of memory formation are becoming more prevalent. Despite this, much remains unknown about the role of sex in this process. We previously reported the first evidence of a novel epigenetic role for proteasome subunit RPT6 during memory formation in the hippocampus of male rodents whereby it associated with monoubiquitinated histone H2B (H2Bubi). Here, we used molecular, biochemical, and behavioral approaches to investigate whether RPT6 has a similar epigenetic role during memory formation in female rats. Following contextual fear conditioning, we found that RPT6 levels and DNA binding at regions coding for c-fos, the previously identified target of RPT6 in males, were unchanged in the hippocampus of females and that loss of RPT6 did not alter learning-induced increases in c-fos However, RPT6 was in complex with H2Bubi in the female hippocampus and this association increased with fear conditioning, suggesting that it could still retain an epigenetic function. Consistent with this, hippocampal siRNA-mediated knockdown of the RPT6-coding gene, Psmc5, impaired memory in females. These results suggest that while RPT6 does associate with epigenetic H2Bubi during memory formation in both males and females, it has sex-specific gene targets during the memory consolidation process.
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Affiliation(s)
- Kayla Farrell
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Aubrey Auerbach
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Timothy J Jarome
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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15
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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16
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Epigenetic Mechanisms in Memory and Cognitive Decline Associated with Aging and Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms222212280. [PMID: 34830163 PMCID: PMC8618067 DOI: 10.3390/ijms222212280] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/21/2022] Open
Abstract
Epigenetic mechanisms, which include DNA methylation, a variety of post-translational modifications of histone proteins (acetylation, phosphorylation, methylation, ubiquitination, sumoylation, serotonylation, dopaminylation), chromatin remodeling enzymes, and long non-coding RNAs, are robust regulators of activity-dependent changes in gene transcription. In the brain, many of these epigenetic modifications have been widely implicated in synaptic plasticity and memory formation. Dysregulation of epigenetic mechanisms has been reported in the aged brain and is associated with or contributes to memory decline across the lifespan. Furthermore, alterations in the epigenome have been reported in neurodegenerative disorders, including Alzheimer’s disease. Here, we review the diverse types of epigenetic modifications and their role in activity- and learning-dependent synaptic plasticity. We then discuss how these mechanisms become dysregulated across the lifespan and contribute to memory loss with age and in Alzheimer’s disease. Collectively, the evidence reviewed here strongly supports a role for diverse epigenetic mechanisms in memory formation, aging, and neurodegeneration in the brain.
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17
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Aykac A, Kalkan R. Epigenetic Approach to PTSD: In the Aspects of Rat Models. Glob Med Genet 2021; 9:7-13. [PMID: 35169777 PMCID: PMC8837403 DOI: 10.1055/s-0041-1736633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/18/2021] [Indexed: 11/04/2022] Open
Abstract
Posttraumatic stress disorder (PTSD) is a stress-related mental disorder and develops after exposure to life-threatening traumatic experiences. The risk factors of PTSD included genetic factors; alterations in hypothalamic–pituitary–adrenal (HPA) axis; neurotrophic, serotonergic, dopaminergic, and catecholaminergic systems; and a variety of environmental factors, such as war, accident, natural disaster, pandemic, physical, or sexual abuse, that cause stress or trauma in individuals. To be able to understand the molecular background of PTSD, rodent animal models are widely used by researchers. When looking for a solution for PTSD, it is important to consider preexisting genetic risk factors and physiological, molecular, and biochemical processes caused by trauma that may cause susceptibility to this disorder. In studies, it is reported that epigenetic mechanisms play important roles in the biological response affected by environmental factors, as well as the task of programming cell identity. In this article, we provided an overview of the role of epigenetic modifications in understanding the biology of PTSD. We also summarized the data from animal studies and their importance during the investigation of PTSD. This study shed light on the epigenetic background of stress and PTSD.
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Affiliation(s)
- Asli Aykac
- Department of Biophysics, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Rasime Kalkan
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Near East University, Nicosia, Cyprus
- Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia, Cyprus
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18
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Trask S, Ferrara NC, Jasnow AM, Kwapis JL. Contributions of the rodent cingulate-retrosplenial cortical axis to associative learning and memory: A proposed circuit for persistent memory maintenance. Neurosci Biobehav Rev 2021; 130:178-184. [PMID: 34450181 PMCID: PMC8511298 DOI: 10.1016/j.neubiorev.2021.08.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 10/20/2022]
Abstract
While the anterior cingulate (ACC) and retrosplenial (RSC) cortices have been extensively studied for their role in spatial navigation, less is known about how they contribute to associative learning and later memory recall. The limited work that has been conducted on this topic suggests that each of these cortical regions makes distinct, but similar contributions to associative learning and memory. Here, we review evidence from the rodent literature demonstrating that while ACC activity seems to be necessary at remote time points associated with imprecise or generalized memories, the role of the RSC seems to be uniform over time. Together, the lines of evidence reviewed here suggest that the ACC and RSC likely function together to support memory formation and maintenance following associative learning.
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Affiliation(s)
- Sydney Trask
- Department of Psychological Sciences, Purdue University, West Lafayette, IN, 47907, United States
| | - Nicole C Ferrara
- Department of Pharmacology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, United States
| | - Aaron M Jasnow
- Department of Pharmacology, Physiology & Neuroscience, University of South Carolina School of Medicine, Columbia, SC, 29209, United States
| | - Janine L Kwapis
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, United States.
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19
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Han JY, Park J. Variable Phenotypes of Epilepsy, Intellectual Disability, and Schizophrenia Caused by 12p13.33-p13.32 Terminal Microdeletion in a Korean Family: A Case Report and Literature Review. Genes (Basel) 2021; 12:genes12071001. [PMID: 34210021 PMCID: PMC8303811 DOI: 10.3390/genes12071001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022] Open
Abstract
A simultaneous analysis of nucleotide changes and copy number variations (CNVs) based on exome sequencing data was demonstrated as a potential new first-tier diagnosis strategy for rare neuropsychiatric disorders. In this report, using depth-of-coverage analysis from exome sequencing data, we described variable phenotypes of epilepsy, intellectual disability (ID), and schizophrenia caused by 12p13.33–p13.32 terminal microdeletion in a Korean family. We hypothesized that CACNA1C and KDM5A genes of the six candidate genes located in this region were the best candidates for explaining epilepsy, ID, and schizophrenia and may be responsible for clinical features reported in cases with monosomy of the 12p13.33 subtelomeric region. On the background of microdeletion syndrome, which was described in clinical cases with mild, moderate, and severe neurodevelopmental manifestations as well as impairments, the clinician may determine whether the patient will end up with a more severe or milder end-phenotype, which in turn determines disease prognosis. In our case, the 12p13.33–p13.32 terminal microdeletion may explain the variable expressivity in the same family. However, further comprehensive studies with larger cohorts focusing on careful phenotyping across the lifespan are required to clearly elucidate the possible contribution of genetic modifiers and the environmental influence on the expressivity of 12p13.33 microdeletion and associated characteristics.
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Affiliation(s)
- Ji Yoon Han
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Korea
- Correspondence: ; Tel.: +82-63-250-1218
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20
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Jarome TJ, Perez GA, Webb WM, Hatch KM, Navabpour S, Musaus M, Farrell K, Hauser RM, McFadden T, Martin K, Butler AA, Wang J, Lubin FD. Ubiquitination of Histone H2B by Proteasome Subunit RPT6 Controls Histone Methylation Chromatin Dynamics During Memory Formation. Biol Psychiatry 2021; 89:1176-1187. [PMID: 33934885 PMCID: PMC8178164 DOI: 10.1016/j.biopsych.2020.12.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 11/29/2020] [Accepted: 12/22/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Posttranslational histone modifications play a critical role in the regulation of gene transcription underlying synaptic plasticity and memory formation. One such epigenetic change is histone ubiquitination, a process that is mediated by the ubiquitin-proteasome system in a manner similar to that by which proteins are normally targeted for degradation. However, histone ubiquitination mechanisms are poorly understood in the brain and in learning. In this article, we describe a new role for the ubiquitin-proteasome system in histone crosstalk, showing that learning-induced monoubiquitination of histone H2B (H2Bubi) is required for increases in the transcriptionally active H3 lysine 4 trimethylation (H3K4me3) mark at learning-related genes in the hippocampus. METHODS Using a series of molecular, biochemical, electrophysiological, and behavioral experiments, we interrogated the effects of short interfering RNA-mediated knockdown and CRISPR (clustered regularly interspaced short palindromic repeats)-mediated upregulation of ubiquitin ligases, deubiquitinating enzymes and histone methyltransferases in the rat dorsal hippocampus during memory consolidation. RESULTS We show that H2Bubi recruits H3K4me3 through a process that is dependent on the 19S proteasome subunit RPT6 and that a loss of H2Bubi in the hippocampus prevents learning-induced increases in H3K4me3, gene transcription, synaptic plasticity, and memory formation. Furthermore, we show that CRISPR-dCas9-mediated increases in H2Bubi promote H3K4me3 and memory formation under weak training conditions and that promoting histone methylation does not rescue memory impairments resulting from loss of H2Bubi. CONCLUSIONS These results suggest that H2B ubiquitination regulates histone crosstalk in learning by way of nonproteolytic proteasome function, demonstrating a novel mechanism by which histone modifications are coordinated in response to learning.
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Affiliation(s)
- Timothy J Jarome
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama; Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, Virginia; School of Neuroscience, Virginia Polytechnic Institute and State University, Roanoke, Virginia; Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Roanoke, Virginia
| | - Gabriella A Perez
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - William M Webb
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Katrina M Hatch
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, Virginia
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Roanoke, Virginia
| | - Kayla Farrell
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Roanoke, Virginia
| | - Rebecca M Hauser
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Taylor McFadden
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Roanoke, Virginia
| | - Kiley Martin
- School of Neuroscience, Virginia Polytechnic Institute and State University, Roanoke, Virginia
| | - Anderson A Butler
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jing Wang
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama.
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21
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Inhibiting MLL1-WDR5 interaction ameliorates neuropathic allodynia by attenuating histone H3 lysine 4 trimethylation-dependent spinal mGluR5 transcription. Pain 2021; 161:1995-2009. [PMID: 32345914 DOI: 10.1097/j.pain.0000000000001898] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 04/20/2020] [Indexed: 01/24/2023]
Abstract
ABSTRACT Mixed lineage leukemia 1 (MLL1)-mediated histone H3 lysine 4 trimethylation (H3K4me3) of a subset of genes has been linked to the transcriptional activation critical for synaptic plasticity, but its potential contribution to neuropathic allodynia development remains poorly explored. Here, we show that MLL1, which is induced in dorsal horn neuron after spinal nerve ligation (SNL), is responsible for mechanical allodynia and increased H3K4me3 at metabotropic glutamate receptor subtype 5 (mGluR5) promoter. Moreover, SNL induced WD (Trp-Asp) repeat domain 5 subunit (WDR5) expression as well as the MLL1-WDR5 interaction accompany with H3K4me3 enrichment and transcription of mGluR5 gene in the dorsal horn in neuropathic allodynia progression. Conversely, WDR5-0103, a novel inhibitor of the MLL1-WDR5 interaction, reversed SNL-induced allodynia and inhibited SNL-enhanced mGluR5 transcription/expression as well as MLL1, WDR5, and H3K4me3 at the mGluR5 promoter in the dorsal horn. Furthermore, disrupting the expression of MLL1 or WDR5 using small interfering RNA attenuated mechanical allodynia and reversed protein transcription/expression and complex localizing at mGluR5 promoter in the dorsal horn induced by SNL. This finding revealed that MLL1-WDR5 complex integrity regulates MLL1 and WDR5 recruitment to H3K4me3 enrichment at mGluR5 promoter in the dorsal horn underlying neuropathic allodynia. Collectively, our findings indicated that SNL enhances the MLL1-WDR5 complex, which facilitates MLL1 and WDR5 recruitment to H3K4me3 enrichment at mGluR5 promoter in spinal plasticity contributing to neuropathic allodynia pathogenesis.
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22
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Devulapalli R, Jones N, Farrell K, Musaus M, Kugler H, McFadden T, Orsi SA, Martin K, Nelsen J, Navabpour S, O'Donnell M, McCoig E, Jarome TJ. Males and females differ in the regulation and engagement of, but not requirement for, protein degradation in the amygdala during fear memory formation. Neurobiol Learn Mem 2021; 180:107404. [PMID: 33609735 DOI: 10.1016/j.nlm.2021.107404] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 02/10/2021] [Indexed: 02/07/2023]
Abstract
Over the last decade, strong evidence has emerged that protein degradation mediated by the ubiquitin-proteasome system is critical for fear memory formation in the amygdala. However, this work has been done primarily in males, leaving unanswered questions about whether females also require protein degradation during fear memory formation. Here, we found that male and female rats differed in their engagement and regulation of, but not need for, protein degradation in the amygdala during fear memory formation. Male, but not female, rats had increased protein degradation in the nuclei of amygdala cells after fear conditioning. Conversely, females had elevated baseline levels of overall ubiquitin-proteasome activity in amygdala nuclei. Gene expression and DNA methylation analyses identified that females had increased baseline expression of the ubiquitin coding gene Uba52, which had increased DNA 5-hydroxymethylation (5hmc) in its promoter region, indicating a euchromatin state necessary for increased levels of ubiquitin in females. Consistent with this, persistent CRISPR-dCas9 mediated silencing of Uba52 and proteasome subunit Psmd14 in the amygdala reduced baseline protein degradation levels and impaired fear memory in male and female rats, while enhancing baseline protein degradation in the amygdala of both sexes promoted fear memory formation. These results suggest that while both males and females require protein degradation in the amygdala for fear memory formation, they differ in their baseline regulation and engagement of this process following learning. These results have important implications for understanding the etiology of sex-related differences in fear memory formation.
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Affiliation(s)
- Rishi Devulapalli
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Natalie Jones
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Kayla Farrell
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Hannah Kugler
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Taylor McFadden
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Sabrina A Orsi
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Kiley Martin
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jacob Nelsen
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Madison O'Donnell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Emmarose McCoig
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Timothy J Jarome
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, USA.
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23
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El Hayek L, Tuncay IO, Nijem N, Russell J, Ludwig S, Kaur K, Li X, Anderton P, Tang M, Gerard A, Heinze A, Zacher P, Alsaif HS, Rad A, Hassanpour K, Abbaszadegan MR, Washington C, DuPont BR, Louie RJ, Couse M, Faden M, Rogers RC, Abou Jamra R, Elias ER, Maroofian R, Houlden H, Lehman A, Beutler B, Chahrour MH. KDM5A mutations identified in autism spectrum disorder using forward genetics. eLife 2020; 9:56883. [PMID: 33350388 PMCID: PMC7755391 DOI: 10.7554/elife.56883] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/06/2020] [Indexed: 12/29/2022] Open
Abstract
Autism spectrum disorder (ASD) is a constellation of neurodevelopmental disorders with high phenotypic and genetic heterogeneity, complicating the discovery of causative genes. Through a forward genetics approach selecting for defective vocalization in mice, we identified Kdm5a as a candidate ASD gene. To validate our discovery, we generated a Kdm5a knockout mouse model (Kdm5a-/-) and confirmed that inactivating Kdm5a disrupts vocalization. In addition, Kdm5a-/- mice displayed repetitive behaviors, sociability deficits, cognitive dysfunction, and abnormal dendritic morphogenesis. Loss of KDM5A also resulted in dysregulation of the hippocampal transcriptome. To determine if KDM5A mutations cause ASD in humans, we screened whole exome sequencing and microarray data from a clinical cohort. We identified pathogenic KDM5A variants in nine patients with ASD and lack of speech. Our findings illustrate the power and efficacy of forward genetics in identifying ASD genes and highlight the importance of KDM5A in normal brain development and function.
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Affiliation(s)
- Lauretta El Hayek
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Islam Oguz Tuncay
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States
| | - Nadine Nijem
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jamie Russell
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Sara Ludwig
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kiran Kaur
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Priscilla Anderton
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States.,Texas Children's Hospital, Houston, United States
| | - Anja Heinze
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Pia Zacher
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.,The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Aboulfazl Rad
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Islamic Republic of Iran
| | - Kazem Hassanpour
- Non-Communicable Diseases Research Center, Sabzevar University of Medical Sciences, Sabzevar, Islamic Republic of Iran
| | - Mohammad Reza Abbaszadegan
- Pardis Clinical and Genetics Laboratory, Mashhad, Islamic Republic of Iran.,Division of Human Genetics, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Islamic Republic of Iran
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- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Madeline Couse
- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Maha Faden
- Department of Genetics, King Saud Medical City, Riyadh, Saudi Arabia
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Ellen R Elias
- Department of Pediatrics and Genetics, University of Colorado School of Medicine, Aurora, United States
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square Institute of Neurology, London, United Kingdom
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, Queen Square Institute of Neurology, London, United Kingdom
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, British Columbia Children's and Women's Hospital Research Institute, Vancouver, Canada
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Maria H Chahrour
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, United States.,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, United States.,Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
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24
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Navabpour S, Rogers J, McFadden T, Jarome TJ. DNA Double-Strand Breaks Are a Critical Regulator of Fear Memory Reconsolidation. Int J Mol Sci 2020; 21:ijms21238995. [PMID: 33256213 PMCID: PMC7730899 DOI: 10.3390/ijms21238995] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022] Open
Abstract
Numerous studies have shown that following retrieval, a previously consolidated memory requires increased transcriptional regulation in order to be reconsolidated. Previously, it was reported that histone H3 lysine-4 trimethylation (H3K4me3), a marker of active transcription, is increased in the hippocampus after the retrieval of contextual fear memory. However, it is currently unknown how this epigenetic mark is regulated during the reconsolidation process. Furthermore, though recent evidence suggests that neuronal activity triggers DNA double-strand breaks (DSBs) in some early-response genes, it is currently unknown if DSBs contribute to the reconsolidation of a memory following retrieval. Here, using chromatin immunoprecipitation (ChIP) analyses, we report a significant overlap between DSBs and H3K4me3 in area CA1 of the hippocampus during the reconsolidation process. We found an increase in phosphorylation of histone H2A.X at serine 139 (H2A.XpS139), a marker of DSB, in the Npas4, but not c-fos, promoter region 5 min after retrieval, which correlated with increased H3K4me3 levels, suggesting that the two epigenetic marks may work in concert during the reconsolidation process. Consistent with this, in vivo siRNA-mediated knockdown of topoisomerase II β, the enzyme responsible for DSB, prior to retrieval, reduced Npas4 promoter-specific H2A.XpS139 and H3K4me3 levels and impaired long-term memory, indicating an indispensable role of DSBs in the memory reconsolidation process. Collectively, our data propose a novel mechanism for memory reconsolidation through increases in epigenetic-mediated transcriptional control via DNA double-strand breaks.
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Affiliation(s)
- Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Translational Biology, Medicine & Health, Virginia Polytechnic Institute and State University, Roanoke, VA 24016, USA;
| | - Jessie Rogers
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Taylor McFadden
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Timothy J. Jarome
- Fralin Biomedical Research Institute, Translational Biology, Medicine & Health, Virginia Polytechnic Institute and State University, Roanoke, VA 24016, USA;
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
- Correspondence: ; Tel.: +1-540-231-3520
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25
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Hu E, Du H, Shang S, Zhang Y, Lu X. Beta-Hydroxybutyrate Enhances BDNF Expression by Increasing H3K4me3 and Decreasing H2AK119ub in Hippocampal Neurons. Front Neurosci 2020; 14:591177. [PMID: 33192276 PMCID: PMC7655964 DOI: 10.3389/fnins.2020.591177] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022] Open
Abstract
Neurological evidence suggests that beta-hydroxybutyrate (BHBA) has positive effects on the central nervous system. Previous studies have explored the molecular mechanisms by which BHBA affects different brain functions, but the effects of BHBA on epigenetic modifications remain elusive. Here, we showed that BHBA enhanced brain-derived neurotrophic factor (BDNF) expression by increasing H3K4me3 and decreasing H2AK119ub occupancy at the Bdnf promoters I, II, IV, and VI in hippocampal neurons. Moreover, BHBA treatment induced the upregulation of H3K4me3 and downregulation of H2AK119ub on the global level, both of which were dependent on the L-type calcium channel. Additionally, the BHBA-activated L-type calcium channel subsequently triggered the activation of Ca2+/CaMKII/CREB signaling, and promoted the binding of p-CREB and CBP to Bdnf promoters. These results indicate that BHBA regulates cellular signaling and multiple histone modifications to cooperatively modulate BDNF, suggesting a wide range of regulatory effects of BHBA in the central nervous system.
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Affiliation(s)
- Erling Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Huan Du
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Sen Shang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yali Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoyun Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an, China
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26
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Borodinova AA, Balaban PM. Epigenetic Regulation as a Basis for Long-Term Changes in the Nervous System: In Search of Specificity Mechanisms. BIOCHEMISTRY (MOSCOW) 2020; 85:994-966. [DOI: 10.1134/s0006297920090023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Adaptive long-term changes in the functioning of nervous system (plasticity, memory) are not written in the genome, but are directly associated with the changes in expression of many genes comprising epigenetic regulation. Summarizing the known data regarding the role of epigenetics in regulation of plasticity and memory, we would like to highlight several key aspects. (i) Different chromatin remodeling complexes and DNA methyltransferases can be organized into high-order multiprotein repressor complexes that are cooperatively acting as the “molecular brake pads”, selectively restricting transcriptional activity of specific genes at rest. (ii) Relevant physiological stimuli induce a cascade of biochemical events in the activated neurons resulting in translocation of different signaling molecules (protein kinases, NO-containing complexes) to the nucleus. (iii) Stimulus-specific nitrosylation and phosphorylation of different epigenetic factors is linked to a decrease in their enzymatic activity or changes in intracellular localization that results in temporary destabilization of the repressor complexes. (iv) Removing “molecular brakes” opens a “critical time window” for global and local epigenetic changes, triggering specific transcriptional programs and modulation of synaptic connections efficiency. It can be assumed that the reversible post-translational histone modifications serve as the basis of plastic changes in the neural network. On the other hand, DNA methylation and methylation-dependent 3D chromatin organization can serve a stable molecular basis for long-term maintenance of plastic changes and memory.
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27
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da Silva TR, Sohn JMB, Andreatini R, Stern CA. The role of prelimbic and anterior cingulate cortices in fear memory reconsolidation and persistence depends on the memory age. Learn Mem 2020; 27:292-300. [PMID: 32669384 PMCID: PMC7365014 DOI: 10.1101/lm.051615.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/01/2020] [Indexed: 01/05/2023]
Abstract
Reconsolidation is a time-limited process under which reactivated memory content can be modified. Works focused on studying reconsolidation mainly restrict intervention to the moments immediately after reactivation and to recently acquired memories. However, the brain areas activated during memory retrieval depend on when it was acquired, and it is relatively unknown how different brain sites contribute to reconsolidation and persistence of reactivated recent and remote fear memories. Here, we sought to investigate the participation of prelimbic (PL) and anterior cingulate cortices (ACC) in recent (1 d old) and remote (21 d old) fear memory reconsolidation and persistence. Male Wistar rats were submitted to the contextual fear conditioning protocol. Tamoxifen (TMX), an estrogen receptor modulator known to inhibit protein kinase C activity was used to interfere with these processes. When infused into the PL cortex, but not into the ACC, TMX administration immediately or 6 h after recent fear memory reactivation impaired memory reconsolidation and persistence, respectively. TMX administered immediately after remote memory reactivation impaired memory reconsolidation when infused into the PL cortex and ACC. However, remote memory persistence was only affected when TMX was infused 6 h after memory reactivation into the ACC and no effect was observed when TMX was infused 6 h after memory reactivation into PL cortex. Together, the findings provide further evidence on the participation of PL cortex and ACC in reconsolidation of recent and remote fear memories and suggest that the persistence of a reactivated fear memory becomes independent on the PL cortex with memory age and dependent on the ACC.
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Affiliation(s)
| | | | - Roberto Andreatini
- Department of Pharmacology, Federal University of Parana, Curitiba 81531-980, Brazil
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28
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Webb WM, Irwin AB, Pepin ME, Henderson BW, Huang V, Butler AA, Herskowitz JH, Wende AR, Cash AE, Lubin FD. The SETD6 Methyltransferase Plays an Essential Role in Hippocampus-Dependent Memory Formation. Biol Psychiatry 2020; 87:577-587. [PMID: 31378303 PMCID: PMC6906268 DOI: 10.1016/j.biopsych.2019.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Epigenetic mechanisms are critical for hippocampus-dependent memory formation. Building on previous studies that implicate the N-lysine methyltransferase SETD6 in the activation of nuclear factor-κB RELA (also known as transcription factor p65) as an epigenetic recruiter, we hypothesized that SETD6 is a key player in the epigenetic control of long-term memory. METHODS Using a series of molecular, biochemical, imaging, electrophysiological, and behavioral experiments, we interrogated the effects of short interfering RNA-mediated knockdown of Setd6 in the rat dorsal hippocampus during memory consolidation. RESULTS Our findings demonstrate that SETD6 is necessary for memory-related nuclear factor-κB RELA methylation at lysine 310 and associated increases in H3K9me2 (histone H3 lysine 9 dimethylation) in the dorsal hippocampus and that SETD6 knockdown interferes with memory consolidation, alters gene expression patterns, and disrupts spine morphology. CONCLUSIONS Together, these findings suggest that SETD6 plays a critical role in memory formation and may act as an upstream initiator of H3K9me2 changes in the hippocampus during memory consolidation.
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Affiliation(s)
- William M Webb
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Ashleigh B Irwin
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Mark E Pepin
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Benjamin W Henderson
- Department of Neurology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Victoria Huang
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Anderson A Butler
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Jeremy H Herskowitz
- Department of Neurology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Adam R Wende
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, Alabama; Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Andrew E Cash
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Farah D Lubin
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, Alabama.
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29
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Navabpour S, Kwapis JL, Jarome TJ. A neuroscientist's guide to transgenic mice and other genetic tools. Neurosci Biobehav Rev 2020; 108:732-748. [PMID: 31843544 PMCID: PMC8049509 DOI: 10.1016/j.neubiorev.2019.12.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/05/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022]
Abstract
The past decade has produced an explosion in the number and variety of genetic tools available to neuroscientists, resulting in an unprecedented ability to precisely manipulate the genome and epigenome in behaving animals. However, no single resource exists that describes all of the tools available to neuroscientists. Here, we review the genetic, transgenic, and viral techniques that are currently available to probe the complex relationship between genes and cognition. Topics covered include types of traditional transgenic mouse models (knockout, knock-in, reporter lines), inducible systems (Cre-loxP, Tet-On, Tet-Off) and cell- and circuit-specific systems (TetTag, TRAP, DIO-DREADD). Additionally, we provide details on virus-mediated and siRNA/shRNA approaches, as well as a comprehensive discussion of the myriad manipulations that can be made using the CRISPR-Cas9 system, including single base pair editing and spatially- and temporally-regulated gene-specific transcriptional control. Collectively, this review will serve as a guide to assist neuroscientists in identifying and choosing the appropriate genetic tools available to study the complex relationship between the brain and behavior.
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Affiliation(s)
- Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Roanoke, VA, USA
| | - Janine L Kwapis
- Department of Biology, Pennsylvania State University, College Park, PA, USA; Center for the Molecular Investigation of Neurological Disorders (CMIND), Pennsylvania State University, College Park, PA, USA.
| | - Timothy J Jarome
- Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Roanoke, VA, USA; Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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30
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Kushwaha A, Thakur MK. Increase in hippocampal histone H3K9me3 is negatively correlated with memory in old male mice. Biogerontology 2019; 21:175-189. [DOI: 10.1007/s10522-019-09850-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/15/2019] [Indexed: 02/08/2023]
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Moretti R, Peinkhofer C. B Vitamins and Fatty Acids: What Do They Share with Small Vessel Disease-Related Dementia? Int J Mol Sci 2019; 20:E5797. [PMID: 31752183 PMCID: PMC6888477 DOI: 10.3390/ijms20225797] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 10/21/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022] Open
Abstract
Many studies have been written on vitamin supplementation, fatty acid, and dementia, but results are still under debate, and no definite conclusion has yet been drawn. Nevertheless, a significant amount of lab evidence confirms that vitamins of the B group are tightly related to gene control for endothelium protection, act as antioxidants, play a co-enzymatic role in the most critical biochemical reactions inside the brain, and cooperate with many other elements, such as choline, for the synthesis of polyunsaturated phosphatidylcholine, through S-adenosyl-methionine (SAM) methyl donation. B-vitamins have anti-inflammatory properties and act in protective roles against neurodegenerative mechanisms, for example, through modulation of the glutamate currents and a reduction of the calcium currents. In addition, they also have extraordinary antioxidant properties. However, laboratory data are far from clinical practice. Many studies have tried to apply these results in everyday clinical activity, but results have been discouraging and far from a possible resolution of the associated mysteries, like those represented by Alzheimer's disease (AD) or small vessel disease dementia. Above all, two significant problems emerge from the research: No consensus exists on general diagnostic criteria-MCI or AD? Which diagnostic criteria should be applied for small vessel disease-related dementia? In addition, no general schema exists for determining a possible correct time of implementation to have effective results. Here we present an up-to-date review of the literature on such topics, shedding some light on the possible interaction of vitamins and phosphatidylcholine, and their role in brain metabolism and catabolism. Further studies should take into account all of these questions, with well-designed and world-homogeneous trials.
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Affiliation(s)
- Rita Moretti
- Neurology Clinic, Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy;
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Zhong J, Xu W. Characterization of DNA hydroxymethylation in the hypothalamus of elderly mice with post-operative cognitive dysfunction. Exp Ther Med 2019; 18:4002-4010. [PMID: 31641381 PMCID: PMC6796353 DOI: 10.3892/etm.2019.8056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/13/2019] [Indexed: 01/12/2023] Open
Abstract
Post-operative cognitive dysfunction (POCD) is a common syndrome characterized by perioperative cerebral damage in elderly patients, including cognitive impairment and memory loss. Recent studies have revealed that anesthesia is one of the key causes of POCD. Ubiquitin-like with PHD and ring finger domains 2 (Uhrf2) has been reported to play a crucial role in regulating DNA methylation and hydroxymethylation, which are closely connected with memory building and erasure. However, whether narcotic drugs can affect Uhrf2 to impact on DNA methylation and hydroxymethylation in POCD is poorly understood. In this study, a POCD model was established in elderly mice through sevoflurane treatment, and these mice were found to have compromised levels of global DNA 5'-hydroxymethylcytosine (5hmC) and Uhrf2 in the hippocampus and the amygdaloid nucleus, when compared with non-POCD and control mice. The results of immunoprecipitation and quantitative PCR revealed that 5hmC modification of the promoters of genes associated with neural protection and development, such as glial cell-derived neurotrophic factor, brain derived neurotrophic factor, glucocorticoid receptor and acyl-CoA sythetase short chain family member 2, was reduced in the hippocampus of POCD mice when compared with non-POCD and control mice. Taken together, the findings of the present study suggest that loss of 5hmC, in the hippocampus and the amygdaloid nucleus modulated by Uhrf2 suppression, may result in the learning and memory ability impairment seen in mice with POCD.
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Affiliation(s)
- Jiang Zhong
- Department of Anesthesiology, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
| | - Wei Xu
- Department of Anesthesiology, Jinshan Hospital, Fudan University, Shanghai 201508, P.R. China
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Hiraide T, Hattori A, Ieda D, Hori I, Saitoh S, Nakashima M, Saitsu H. De novo variants in SETD1B cause intellectual disability, autism spectrum disorder, and epilepsy with myoclonic absences. Epilepsia Open 2019; 4:476-481. [PMID: 31440728 PMCID: PMC6698685 DOI: 10.1002/epi4.12339] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/27/2019] [Accepted: 05/09/2019] [Indexed: 02/02/2023] Open
Abstract
Epilepsy with myoclonic absences is a specific seizure type characterized by bilateral rhythmic clonic jerks with impairment of consciousness. Here, we report an individual with epilepsy with myoclonic absences, mild intellectual disabilities, language disorder, and autism spectrum disorder. His interictal electroencephalogram revealed a spike-and-slow wave complex dominant in the frontal area. His ictal polygraphic and video-electroencephalogram showed a characteristic diffuse synchronous 3-Hz spike-and-wave burst associated with bilateral upper limb myoclonic jerks with impairment of consciousness. Using whole-exome sequencing, we found a novel de novo variant, c.386T>G, p.(Val129Gly), in SETD1B (SET domain containing 1B). We previously reported that two individuals with a de novo SETD1B variant showed intellectual disability, epilepsy, and autism. Of note, one of those individuals and the present case showed epilepsy with myoclonic absences. Therefore, this report supports the indication that SETD1B may be a causative gene for neurodevelopmental disorders and suggests that epilepsy with myoclonic absences may be a characteristic feature of SETD1B-related disorders.
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Affiliation(s)
- Takuya Hiraide
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
- Department of PediatricsHamamatsu University School of MedicineHamamatsuJapan
| | - Ayako Hattori
- Department of Pediatrics and NeonatologyNagoya City University, Graduate School of Medical SciencesAichiJapan
| | - Daisuke Ieda
- Department of Pediatrics and NeonatologyNagoya City University, Graduate School of Medical SciencesAichiJapan
| | - Ikumi Hori
- Department of Pediatrics and NeonatologyNagoya City University, Graduate School of Medical SciencesAichiJapan
| | - Shinji Saitoh
- Department of Pediatrics and NeonatologyNagoya City University, Graduate School of Medical SciencesAichiJapan
| | - Mitsuko Nakashima
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
| | - Hirotomo Saitsu
- Department of BiochemistryHamamatsu University School of MedicineHamamatsuJapan
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Keiser AA, Wood MA. Examining the contribution of histone modification to sex differences in learning and memory. Learn Mem 2019; 26:318-331. [PMID: 31416905 PMCID: PMC6699407 DOI: 10.1101/lm.048850.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/08/2019] [Indexed: 01/04/2023]
Abstract
The epigenome serves as a signal integration platform that encodes information from experience and environment that adds tremendous complexity to the regulation of transcription required for memory, beyond the directions encoded in the genome. To date, our understanding of how epigenetic mechanisms integrate information to regulate gene expression required for memory is primarily obtained from male derived data despite sex-specific life experiences and sex differences in consolidation and retrieval of memory, and in the molecular mechanisms that mediate these processes. In this review, we examine the contribution of chromatin modification to learning and memory in both sexes. We provide examples of how exposure to a number of internal and external factors influence the epigenome in sex-similar and sex-specific ways that may ultimately impact transcription required for memory processes. We also pose a number of key open questions and identify areas requiring further investigation as we seek to understand how histone modifying mechanisms shape memory in females.
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Affiliation(s)
- Ashley A Keiser
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, California 92697, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, California 92697, USA
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Wang Z, Liu H. Lysine methylation regulates nervous system diseases. Neuropeptides 2019; 76:101929. [PMID: 31076097 DOI: 10.1016/j.npep.2019.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 04/27/2019] [Accepted: 04/28/2019] [Indexed: 12/17/2022]
Abstract
Lysine methylation is an important dynamic modification which is essential in the epigenetic regulation of gene transcription. Unlike acetylation markers, lysine methylation signals at gene promoters could be viewed as markers that either activate or silence gene expression in different contexts or states. This article briefly reviews lysine methylation sites involved in nervous system diseases. The methyltransferases and demethylases which cause abnormal methylation signals in nervous system diseases are also discussed. Methylated proteins correlated with nervous system biological processes are extracted from databases and known writer-code-eraser patterns are analyzed, which could provide insight into the design of methylation-based interference peptides for the investigation of nervous system diseases.
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Affiliation(s)
- Zhen Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science, Xi'an Jiaotong University, Xi'an 710049, China.
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Sánchez RG, Parrish RR, Rich M, Webb WM, Lockhart RM, Nakao K, Ianov L, Buckingham SC, Broadwater DR, Jenkins A, de Lanerolle NC, Cunningham M, Eid T, Riley K, Lubin FD. Human and rodent temporal lobe epilepsy is characterized by changes in O-GlcNAc homeostasis that can be reversed to dampen epileptiform activity. Neurobiol Dis 2019; 124:531-543. [PMID: 30625365 PMCID: PMC6379093 DOI: 10.1016/j.nbd.2019.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/26/2018] [Accepted: 01/01/2019] [Indexed: 02/06/2023] Open
Abstract
Temporal Lobe Epilepsy (TLE) is frequently associated with changes in protein composition and post-translational modifications (PTM) that exacerbate the disorder. O-linked-β-N-acetyl glucosamine (O-GlcNAc) is a PTM occurring at serine/threonine residues that is derived from and closely associated with metabolic substrates. The enzymes O-GlcNActransferase (OGT) and O-GlcNAcase (OGA) mediate the addition and removal, respectively, of the O-GlcNAc modification. The goal of this study was to characterize OGT/OGA and protein O-GlcNAcylation in the epileptic hippocampus and to determine and whether direct manipulation of these proteins and PTM's alter epileptiform activity. We observed reduced global and protein specific O-GlcNAcylation and OGT expression in the kainate rat model of TLE and in human TLE hippocampal tissue. Inhibiting OGA with Thiamet-G elevated protein O-GlcNAcylation, and decreased both seizure duration and epileptic spike events, suggesting that OGA may be a therapeutic target for seizure control. These findings suggest that loss of O-GlcNAc homeostasis in the kainate model and in human TLE can be reversed via targeting of O-GlcNAc related pathways.
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Affiliation(s)
- Richard G Sánchez
- Department of Neurobiology, University of Alabama, Birmingham, AL, United States
| | - R Ryley Parrish
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Megan Rich
- Department of Neurobiology, University of Alabama, Birmingham, AL, United States
| | - William M Webb
- Department of Neurobiology, University of Alabama, Birmingham, AL, United States
| | - Roxanne M Lockhart
- Department of Neurobiology, University of Alabama, Birmingham, AL, United States
| | - Kazuhito Nakao
- Department of Neurobiology, University of Alabama, Birmingham, AL, United States
| | - Lara Ianov
- Civitan International Research Center, University of Alabama, Birmingham, AL, United States
| | - Susan C Buckingham
- Department of Neurobiology, University of Alabama, Birmingham, AL, United States
| | - Devin R Broadwater
- School of Medicine, University of Alabama, Birmingham, AL, United States
| | - Alistair Jenkins
- Department of Neurosurgery, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK
| | - Nihal C de Lanerolle
- Department of Laboratory Medicine and of Neurosurgery, Yale School of Medicine, New Haven, CT, United States
| | - Mark Cunningham
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Tore Eid
- Department of Laboratory Medicine and of Neurosurgery, Yale School of Medicine, New Haven, CT, United States
| | - Kristen Riley
- Department of Neurosurgery, University of Alabama, Birmingham, AL, United States
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama, Birmingham, AL, United States.
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Abstract
In the past few decades, the field of neuroepigenetics has investigated how the brain encodes information to form long-lasting memories that lead to stable changes in behaviour. Activity-dependent molecular mechanisms, including, but not limited to, histone modification, DNA methylation and nucleosome remodelling, dynamically regulate the gene expression required for memory formation. Recently, the field has begun to examine how a learning experience is integrated at the level of both chromatin structure and synaptic physiology. Here, we provide an overview of key established epigenetic mechanisms that are important for memory formation. We explore how epigenetic mechanisms give rise to stable alterations in neuronal function by modifying synaptic structure and function, and highlight studies that demonstrate how manipulating epigenetic mechanisms may push the boundaries of memory.
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Affiliation(s)
- Rianne R Campbell
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, Center for Addiction Neuroscience, Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, Center for Addiction Neuroscience, Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA.
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Glover ME, McCoy CR, Shupe EA, Unroe KA, Jackson NL, Clinton SM. Perinatal exposure to the SSRI paroxetine alters the methylome landscape of the developing dentate gyrus. Eur J Neurosci 2019; 50:1843-1870. [PMID: 30585666 DOI: 10.1111/ejn.14315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 11/28/2018] [Accepted: 12/12/2018] [Indexed: 12/24/2022]
Abstract
Evidence in humans and rodents suggests that perinatal exposure to selective serotonin reuptake inhibitor (SSRI) antidepressants can have serious long-term consequences in offspring exposed in utero or infancy via breast milk. In spite of this, there is limited knowledge of how perinatal SSRI exposure impacts brain development and adult behaviour. Children exposed to SSRIs in utero exhibit increased internalizing behaviour and abnormal social behaviour between the ages of 3 and 6, and increased risk of depression in adolescence; however, the neurobiological changes underlying this behaviour are poorly understood. In rodents, perinatal SSRI exposure perturbs hippocampal gene expression and alters adult emotional behaviour (including increased depression-like behaviour). The present study demonstrates that perinatal exposure to the SSRI paroxetine leads to DNA hypomethylation and reduces DNA methyltransferase 3a (Dnmt3a) mRNA expression in the hippocampus during the second and third weeks of life. Next-generation sequencing identified numerous differentially methylated genomic regions, including altered methylation and transcription of several dendritogenesis-related genes. We then tested the hypothesis that transiently decreasing Dnmt3a expression in the early postnatal hippocampus would mimic the behavioural effects of perinatal SSRI exposure. We found that siRNA-mediated knockdown of Dnmt3a in the dentate gyrus during the second to third week of life produced greater depression-like behaviour in adult female (but not male) offspring, akin to the behavioural consequences of perinatal SSRI exposure. Overall, these data suggest that perinatal SSRI exposure may increase depression-like behaviours, at least in part, through reduced Dnmt3a expression in the developing hippocampus.
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Affiliation(s)
| | | | | | - Keaton A Unroe
- School of Neuroscience, Virginia Tech, Blacksburg, Virginia
| | - Nateka L Jackson
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
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Collins BE, Greer CB, Coleman BC, Sweatt JD. Histone H3 lysine K4 methylation and its role in learning and memory. Epigenetics Chromatin 2019; 12:7. [PMID: 30616667 PMCID: PMC6322263 DOI: 10.1186/s13072-018-0251-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
Epigenetic modifications such as histone methylation permit change in chromatin structure without accompanying change in the underlying genomic sequence. A number of studies in animal models have shown that dysregulation of various components of the epigenetic machinery causes cognitive deficits at the behavioral level, suggesting that proper epigenetic control is necessary for the fundamental processes of learning and memory. Histone H3 lysine K4 (H3K4) methylation comprises one component of such epigenetic control, and global levels of this mark are increased in the hippocampus during memory formation. Modifiers of H3K4 methylation are needed for memory formation, shown through animal studies, and many of the same modifiers are mutated in human cognitive diseases. Indeed, all of the known H3K4 methyltransferases and four of the known six H3K4 demethylases have been associated with impaired cognition in a neurologic or psychiatric disorder. Cognitive impairment in such patients often manifests as intellectual disability, consistent with a role for H3K4 methylation in learning and memory. As a modification quintessentially, but not exclusively, associated with transcriptional activity, H3K4 methylation provides unique insights into the regulatory complexity of writing, reading, and erasing chromatin marks within an activated neuron. The following review will discuss H3K4 methylation and connect it to transcriptional events required for learning and memory within the developed nervous system. This will include an initial discussion of the most recent advances in the developing methodology to analyze H3K4 methylation, namely mass spectrometry and deep sequencing, as well as how these methods can be applied to more deeply understand the biology of this mark in the brain. We will then introduce the core enzymatic machinery mediating addition and removal of H3K4 methylation marks and the resulting epigenetic signatures of these marks throughout the neuronal genome. We next foray into the brain, discussing changes in H3K4 methylation marks within the hippocampus during memory formation and retrieval, as well as the behavioral correlates of H3K4 methyltransferase deficiency in this region. Finally, we discuss the human cognitive diseases connected to each H3K4 methylation modulator and summarize advances in developing drugs to target them.
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Affiliation(s)
- Bridget E Collins
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Celeste B Greer
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - Benjamin C Coleman
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA
| | - J David Sweatt
- Department of Pharmacology, Vanderbilt University, 2220 Pierce Avenue, Nashville, TN, 37232, USA.
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Albo Z, Gräff J. The mysteries of remote memory. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0029. [PMID: 29352028 PMCID: PMC5790827 DOI: 10.1098/rstb.2017.0029] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2017] [Indexed: 12/16/2022] Open
Abstract
Long-lasting memories form the basis of our identity as individuals and lie central in shaping future behaviours that guide survival. Surprisingly, however, our current knowledge of how such memories are stored in the brain and retrieved, as well as the dynamics of the circuits involved, remains scarce despite seminal technical and experimental breakthroughs in recent years. Traditionally, it has been proposed that, over time, information initially learnt in the hippocampus is stored in distributed cortical networks. This process-the standard theory of memory consolidation-would stabilize the newly encoded information into a lasting memory, become independent of the hippocampus, and remain essentially unmodifiable throughout the lifetime of the individual. In recent years, several pieces of evidence have started to challenge this view and indicate that long-lasting memories might already ab ovo be encoded, and subsequently stored in distributed cortical networks, akin to the multiple trace theory of memory consolidation. In this review, we summarize these recent findings and attempt to identify the biologically plausible mechanisms based on which a contextual memory becomes remote by integrating different levels of analysis: from neural circuits to cell ensembles across synaptic remodelling and epigenetic modifications. From these studies, remote memory formation and maintenance appear to occur through a multi-trace, dynamic and integrative cellular process ranging from the synapse to the nucleus, and represent an exciting field of research primed to change quickly as new experimental evidence emerges.This article is part of a discussion meeting issue 'Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists'.
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Affiliation(s)
- Zimbul Albo
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Féderale Lausanne, CH-1015 Lausanne, Switzerland
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Féderale Lausanne, CH-1015 Lausanne, Switzerland
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Acute and long-lasting effects of oxytocin in cortico-limbic circuits: consequences for fear recall and extinction. Psychopharmacology (Berl) 2019; 236:339-354. [PMID: 30302511 DOI: 10.1007/s00213-018-5030-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/05/2018] [Indexed: 12/11/2022]
Abstract
The extinction of conditioned fear responses entrains the formation of safe new memories to decrease those behavioral responses. The knowledge in neuronal mechanisms of extinction is fundamental in the treatment of anxiety and fear disorders. Interestingly, the use of pharmacological compounds that reduce anxiety and fear has been shown as a potent co-adjuvant in extinction therapy. However, the efficiency and mechanisms by which pharmacological compounds promote extinction of fear memories remains still largely unknown and would benefit from a validation based on functional neuronal circuits, and the neurotransmitters that modulate them. From this perspective, oxytocin receptor signaling, which has been shown in cortical and limbic areas to modulate numerous functions (Eliava et al. Neuron 89(6):1291-1304, 2016), among them fear and anxiety circuits, and to enhance the salience of social stimuli (Stoop Neuron 76(1):142-59, 2012), may offer an interesting perspective. Experiments in animals and humans suggest that oxytocin could be a promising pharmacological agent at adjusting memory consolidation to boost fear extinction. Additionally, it is possible that long-term changes in endogenous oxytocin signaling can also play a role in reducing expression of fear at different brain targets. In this review, we summarize the effects reported for oxytocin in cortico-limbic circuits and on fear behavior that are of relevance for the modulation and potential extinction of fear memories.
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Marshall PR, Bredy TW. Neuroepigenetic mechanisms underlying fear extinction: emerging concepts. Psychopharmacology (Berl) 2019; 236:133-142. [PMID: 30506235 PMCID: PMC7293886 DOI: 10.1007/s00213-018-5084-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022]
Abstract
An understanding of how memory is acquired and how it can be modified in fear-related anxiety disorders, with the enhancement of failing memories on one side and a reduction or elimination of traumatic memories on the other, is a key unmet challenge in the fields of neuroscience and neuropsychiatry. The latter process depends on an important form of learning called fear extinction, where a previously acquired fear-related memory is decoupled from its ability to control behaviour through repeated non-reinforced exposure to the original fear-inducing cue. Although simple in description, fear extinction relies on a complex pattern of brain region and cell-type specific processes, some of which are unique to this form of learning and, for better or worse, contribute to the inherent instability of fear extinction memory. Here, we explore an emerging layer of biology that may compliment and enrich the synapse-centric perspective of fear extinction. As opposed to the more classically defined role of protein synthesis in the formation of fear extinction memory, a neuroepigenetic view of the experience-dependent gene expression involves an appreciation of dynamic changes in the state of the entire cell: from a transient change in plasticity at the level of the synapse, to potentially more persistent long-term effects within the nucleus. A deeper understanding of neuroepigenetic mechanisms and how they influence the formation and maintenance of fear extinction memory has the potential to enable the development of more effective treatment approaches for fear-related neuropsychiatric conditions.
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Affiliation(s)
- Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
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43
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Orsi SA, Devulapalli RK, Nelsen JL, McFadden T, Surineni R, Jarome TJ. Distinct subcellular changes in proteasome activity and linkage-specific protein polyubiquitination in the amygdala during the consolidation and reconsolidation of a fear memory. Neurobiol Learn Mem 2018; 157:1-11. [PMID: 30458285 DOI: 10.1016/j.nlm.2018.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/30/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022]
Abstract
Numerous studies have supported a critical role for the ubiquitin-proteasome system (UPS) in the memory consolidation and reconsolidation processes. The protein targets and functional role of ubiquitin-proteasome activity can vary widely across cellular compartments, however, it is unknown how UPS activity changes within the nuclear, cytoplasmic, and synaptic regions in response to learning or memory retrieval. Additionally, while previous studies have focused on degradation-specific protein polyubiquitination, it is unknown how learning alters other polyubiquitin tags that are not targeted by the proteasome. Using cellular fractionation protocols in combination with linkage-specific polyubiquitin antibodies, we examined subcellular changes in ubiquitin-proteasome activity in the amygdala during memory consolidation and reconsolidation. Following memory acquisition, overall protein ubiquitination and proteasome activity simultaneously increased in the nucleus and decreased in the synaptic and cytoplasmic regions. The nuclear increases were associated with upregulation of degradation-specific (K48) and degradation-independent (K63, M1) polyubiquitin tags, suggesting multiple functions for ubiquitin signaling within this region. Interestingly, retrieval induced a very different pattern of ubiquitin-proteasome activity in the amygdala, consisting of increases in overall protein ubiquitination and proteasome activity and K48-, K63-, and M1-polyubiquitin tags in the synaptic, but not nuclear or cytoplasmic regions. Collectively, learning and memory retrieval dynamically and differentially alter degradation-dependent and degradation-independent ubiquitin-proteasome activity across different cellular compartments, suggesting that the UPS may serve unique functions during memory consolidation and reconsolidation.
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Affiliation(s)
- Sabrina A Orsi
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Rishi K Devulapalli
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jacob L Nelsen
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Taylor McFadden
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Rithika Surineni
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Timothy J Jarome
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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Kyrke-Smith M, Williams JM. Bridging Synaptic and Epigenetic Maintenance Mechanisms of the Engram. Front Mol Neurosci 2018; 11:369. [PMID: 30344478 PMCID: PMC6182070 DOI: 10.3389/fnmol.2018.00369] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/18/2018] [Indexed: 12/27/2022] Open
Abstract
How memories are maintained, and how memories are lost during aging or disease, are intensely investigated issues. Arguably, the reigning theory is that synaptic modifications allow for the formation of engrams during learning, and sustaining engrams sustains memory. Activity-regulated gene expression profiles have been shown to be critical to these processes, and their control by the epigenome has begun to be investigated in earnest. Here, we propose a novel theory as to how engrams are sustained. We propose that many of the genes that are currently believed to underlie long-term memory are actually part of a “plasticity transcriptome” that underpins structural and functional modifications to neuronal connectivity during the hours to days following learning. Further, we hypothesize that a “maintenance transcriptome” is subsequently induced that includes epigenetic negative regulators of gene expression, particularly histone deacetylases. The maintenance transcriptome negatively regulates the plasticity transcriptome, and thus the plastic capability of a neuron, after learning. In this way, the maintenance transcriptome would act as a metaplasticity mechanism that raises the threshold for change in neurons within an engram, helping to ensure the connectivity is stabilized and memory is maintained.
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Affiliation(s)
- Madeleine Kyrke-Smith
- Department of Anatomy, The Brain Health Research Centre, Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand.,Department of Psychology, The Brain Health Research Centre, Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand.,Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
| | - Joanna M Williams
- Department of Anatomy, The Brain Health Research Centre, Brain Research New Zealand - Rangahau Roro Aotearoa, University of Otago, Dunedin, New Zealand
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EZH2 Methyltransferase Activity Controls Pten Expression and mTOR Signaling during Fear Memory Reconsolidation. J Neurosci 2018; 38:7635-7648. [PMID: 30030400 DOI: 10.1523/jneurosci.0538-18.2018] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 06/20/2018] [Accepted: 07/07/2018] [Indexed: 12/11/2022] Open
Abstract
Memory retrieval induces a transient period of increased transcriptional and translational regulation in neurons called reconsolidation, which is regulated by the protein kinase B (AKT)-mammalian target of rapamycin (mTOR) pathway. However, it is currently unknown how activation of the AKT-mTOR pathway is regulated during the reconsolidation process. Here, we found that in male rats retrieval of a contextual fear memory transiently increased Enhancer of Zeste Homolog 2 (EZH2) levels along with increased histone H3 lysine 27 trimethylation (H3K27me3) levels, which correlated with decreased levels of phosphatase and tensin homolog (PTEN), a potent inhibitor of AKT-mTOR-dependent signaling in the hippocampus. Further experiments found increased H3K27me3 levels and DNA methylation across the Pten promoter and coding regions, indicating transcriptional silencing of the Pten gene. Pten H3K27me3 levels did not change following training or after the retrieval of a remote (old) fear memory, suggesting that this mechanism of Pten repression was specific to the reconsolidation of a new memory. In vivo siRNA-mediated knockdown of Ezh2 in the hippocampus abolished retrieval-induced increases in H3K27me3 and prevented decreases in PTEN levels. Ezh2 knockdown attenuated increases in the phosphorylation of AKT and mTOR following retrieval, which could be restored by simultaneously reducing Pten, suggesting that H3K27me3 regulates AKT-mTOR phosphorylation via repression of Pten Consistent with these results, knockdown of Ezh2 in area CA1 before retrieval impaired memory on later tests. Collectively, these results suggest that EZH2-mediated H3K27me3 plays a critical role in the repression of Pten transcription necessary for AKT-mTOR activation and memory reconsolidation following retrieval.SIGNIFICANCE STATEMENT Understanding how critical translation pathways, like mTOR-mediated protein synthesis, are regulated during the memory storage process is necessary for improving memory impairments. This study tests whether mTOR activation is coupled to epigenetic mechanisms in the hippocampus following the retrieval of a contextual fear memory. Specifically, this study evaluates the role of epigenetic modifications in the form of histone methylation in downstream mTOR translational control during learning-dependent synaptic plasticity in neurons. Considering the broad implications of transcriptional and translational mechanisms in synaptic plasticity, psychiatric, and neurological and neurodegenerative disorders, these data are of interest to the neuroscience community due to the robust and specific regulation of mTOR signaling we found to be dependent on repressive histone methylation.
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Kumar R, Jain V, Kushwah N, Dheer A, Mishra KP, Prasad D, Singh SB. Role of DNA Methylation in Hypobaric Hypoxia-Induced Neurodegeneration and Spatial Memory Impairment. Ann Neurosci 2018; 25:191-200. [PMID: 31000957 DOI: 10.1159/000490368] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/24/2018] [Indexed: 12/19/2022] Open
Abstract
Hypobaric hypoxia (HH) is a major stress factor that is associated with physiological, biochemical, molecular and genomic alterations. Brain is the organ that reacts sensitively to oxygen deprivation, which leads to oxidative stress and cognitive function impairment. Our previous studies have reported that downregulation of brain derived neurotrophic factor (BDNF) leads to neurodegeneration and memory impairment. The aim of the present study was to investigate the effect of HH exposure on DNA methylation and its regulation in BDNF expression, neurodegeneration and spatial memory impairment. For this purpose, Sprague Dawley rats were exposed to HH at a simulated altitude of 25,000 feet for 14 days. Real-time polymerase chain reaction was used for transcriptional expression of DNA Methyltransferases (DNMTs) including DNMT1, DNMT3a and -DNMT3b, and immunoblotting was used for the translational expression of DNMT1, DNMT3a, DNMT3b, Methyl CpG binding protein 2 (MeCP2), pMeCP2 and BDNF in rat hippocampus. Additionally, neuronal morphology alteration and neurodegeneration in CA1 region of hippocampus were investigated though Cresyl violet (CV) staining and Fluoro-Jade C staining respectively. Results obtained suggested that HH exposure increased the expression of DNMT1 DNMT3b at the mRNA as well as protein level, whereas no significant change was observed in the level of DNMT3a. Furthermore, the level of pMeCP2 and BDNF were significantly decreased; however, the expression level of MeCP2 was significantly increased. The CV and Fluoro-Jade C-positive cells were significantly enhanced in the CA1 region of hippocampus in the HH exposed group as compared to unexposed rats. Thus, the present study concluded that HH decreases neuronal activation by the upregulation of DNA methylation and MeCP2 and decreased the expression of pMeCP2, which result in the downregulation of BDNF. The decreased BDNF expression is associated with neuronal loss and spatial memory impairment. This study highlights that DNMT inhibition could be an important therapeutic target for neurodegenerative diseases.
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Affiliation(s)
- Rahul Kumar
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Vishal Jain
- Neurophysiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Neetu Kushwah
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Aastha Dheer
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Kamla Prasad Mishra
- Directorate General Life Sciences, Defence research Development Organisation (DRDO), Government of India, DRDO Bhawan, Rajaji Marg, New Delhi, India
| | - Dipti Prasad
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Shashi Bala Singh
- Directorate General Life Sciences, Defence research Development Organisation (DRDO), Government of India, DRDO Bhawan, Rajaji Marg, New Delhi, India
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Kim GS, Smith AK, Nievergelt CM, Uddin M. Neuroepigenetics of Post-Traumatic Stress Disorder. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:227-253. [PMID: 30072055 PMCID: PMC6474244 DOI: 10.1016/bs.pmbts.2018.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While diagnosis of PTSD is based on behavioral symptom clusters that are most directly associated with brain function, epigenetic studies of PTSD in humans to date have been limited to peripheral tissues. Animal models of PTSD have been key for understanding the epigenetic alterations in the brain most directly relevant to endophenotypes of PTSD, in particular those pertaining to fear memory and stress response. This chapter provides an overview of neuroepigenetic studies based on animal models of PTSD, with an emphasis on the effect of stress on fear memory. Where relevant, we also describe human-based studies with relevance to neuroepigenetic insights gleaned from animal work and suggest promising directions for future studies of PTSD neuroepigenetics in living humans that combine peripheral epigenetic measures with measures of central nervous system activity, structure and function.
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Affiliation(s)
- Grace S Kim
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Medical Scholars Program, University of Illinois College of Medicine, Urbana, IL, United States
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, United States; Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, United States
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, United States
| | - Monica Uddin
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Department of Psychology, University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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Jarome TJ, Devulapalli RK. The Ubiquitin-Proteasome System and Memory: Moving Beyond Protein Degradation. Neuroscientist 2018. [DOI: 10.1177/1073858418762317] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cellular models of memory formation have focused on the need for protein synthesis. Recently, evidence has emerged that protein degradation mediated by the ubiquitin-proteasome system (UPS) is also important for this process. This has led to revised cellular models of memory formation that focus on a balance between protein degradation and synthesis. However, protein degradation is only one function of the UPS. Studies using single-celled organisms have shown that non-proteolytic ubiquitin-proteasome signaling is involved in histone modifications and DNA methylation, suggesting that ubiquitin and the proteasome can regulate chromatin remodeling independent of protein degradation. Despite this evidence, the idea that the UPS is more than a protein degradation pathway has not been examined in the context of memory formation. In this article, we summarize recent findings implicating protein degradation in memory formation and discuss various ways in which both ubiquitin signaling and the proteasome could act independently to regulate epigenetic-mediated transcriptional processes necessary for learning-dependent synaptic plasticity. We conclude by proposing comprehensive models of how non-proteolytic functions of the UPS could work in concert to control epigenetic regulation of the cellular memory consolidation process, which will serve as a framework for future studies examining the role of the UPS in memory formation.
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Affiliation(s)
- Timothy J. Jarome
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Rishi K. Devulapalli
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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Akers KG, Chérasse Y, Fujita Y, Srinivasan S, Sakurai T, Sakaguchi M. Concise Review: Regulatory Influence of Sleep and Epigenetics on Adult Hippocampal Neurogenesis and Cognitive and Emotional Function. Stem Cells 2018; 36:969-976. [DOI: 10.1002/stem.2815] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 02/02/2018] [Accepted: 02/17/2018] [Indexed: 12/20/2022]
Affiliation(s)
| | - Yoan Chérasse
- International Institute for Integrative Sleep Medicine, University of Tsukuba; Tsukuba Ibaraki Japan
| | - Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine; Osaka University; Suita Osaka Japan
| | - Sakthivel Srinivasan
- International Institute for Integrative Sleep Medicine, University of Tsukuba; Tsukuba Ibaraki Japan
| | - Takeshi Sakurai
- International Institute for Integrative Sleep Medicine, University of Tsukuba; Tsukuba Ibaraki Japan
| | - Masanori Sakaguchi
- International Institute for Integrative Sleep Medicine, University of Tsukuba; Tsukuba Ibaraki Japan
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50
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Epigenetic Etiology of Intellectual Disability. J Neurosci 2017; 37:10773-10782. [PMID: 29118205 DOI: 10.1523/jneurosci.1840-17.2017] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/26/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022] Open
Abstract
Intellectual disability (ID) is a prevailing neurodevelopmental condition associated with impaired cognitive and adaptive behaviors. Many chromatin-modifying enzymes and other epigenetic regulators have been genetically associated with ID disorders (IDDs). Here we review how alterations in the function of histone modifiers, chromatin remodelers, and methyl-DNA binding proteins contribute to neurodevelopmental defects and altered brain plasticity. We also discuss how progress in human genetics has led to the generation of mouse models that unveil the molecular etiology of ID, and outline the direction in which this field is moving to identify therapeutic strategies for IDDs. Importantly, because the chromatin regulators linked to IDDs often target common downstream genes and cellular processes, the impact of research in individual syndromes goes well beyond each syndrome and can also contribute to the understanding and therapy of other IDDs. Furthermore, the investigation of these disorders helps us to understand the role of chromatin regulators in brain development, plasticity, and gene expression, thereby answering fundamental questions in neurobiology.
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