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Min EK, Kim SR, Lee CM, Na KH, Park CH, Oh BC, Jung Y, Hong IS. Identification of memory mechanism in tissue-resident stem cells via ANGPTL4 beyond immune cells upon viral antigen exposure. Mol Ther 2024; 32:3042-3058. [PMID: 38582960 PMCID: PMC11403228 DOI: 10.1016/j.ymthe.2024.04.006] [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: 01/11/2024] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024] Open
Abstract
Although memory functions of immune cells characterized by increased resistance to subsequent infections after initial pathogen exposure are well-established, it remains unclear whether non-immune cells, especially tissue-resident stem cells, exhibit similar memory mechanisms. The present study revealed that detrimental effects of initial viral antigen exposure (human papillomavirus [HPV]) on diverse stem cell functions were significantly exacerbated upon subsequent secondary exposure both in vitro and in vivo. Importantly, endometrial stem cells exhibited robust memory functions following consecutive HPV antigen exposures, whereas fully differentiated cells such as fibroblasts and vesicular cells did not show corresponding changes in response to the same antigen exposures. Deficiency of angiopoietin-like 4 (ANGPTL4) achieved through small hairpin RNA knockdown in vitro and knockout (KO) mice in vivo highlighted the critical role of ANGPTL4 in governing memory functions associated with various stem cell processes. This regulation occurred through histone H3 methylation alterations and PI3K/Akt signaling pathways in response to successive HPV antigen exposures. Furthermore, memory functions associated with various stem cell functions that were evident in wild-type mice following consecutive exposures to HPV antigen were not observed in ANGPTL4 KO mice. In summary, our findings strongly support the presence of memory mechanism in non-immune cells, particularly tissue-resident stem cells.
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Affiliation(s)
- Eun-Kyung Min
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Republic of Korea
| | - Soo-Rim Kim
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Republic of Korea
| | - Choon-Mi Lee
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Republic of Korea
| | - Kun-Hee Na
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Microbiology, College of Medicine, Gachon University, Incheon 21999, Korea
| | - Chan Hum Park
- Department of Otolaryngology-Head and Neck Surgery, Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon, Republic of Korea
| | - Byung-Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon 21999, Republic of Korea
| | - YunJae Jung
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Microbiology, College of Medicine, Gachon University, Incheon 21999, Korea.
| | - In-Sun Hong
- Department of Health Sciences and Technology, GAIHST, Gachon University, Incheon 21999, Republic of Korea; Department of Molecular Medicine, School of Medicine, Gachon University, Incheon 406-840, Republic of Korea.
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Park S, Min E, Kim S, Kim S, Na K, Park CH, Jung Y, Oh B, Hong I. Exploring Memory Function Beyond Immune Cells: ANGPTL4-Mediated Memory Functions in Tissue Resident Stem Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307545. [PMID: 38666393 PMCID: PMC11267307 DOI: 10.1002/advs.202307545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/15/2024] [Indexed: 07/25/2024]
Abstract
Adapted immune cells are known to develop memory functions that increase resistance to subsequent infections after initial pathogen exposure, however, it is unclear whether non-immune cells, like tissue-resident stem cells, have similar memory functions. Here, it is found that tissue-resident stem cells crucial for tissue regeneration show diminished adverse effects on diverse stem cell functions against successive exposure to foreign antigen (β-glucan) to maintain tissue homeostasis and stability both in vitro and in vivo. These data suggest that endometrial stem cells may possess a robust memory function, in contrast, fully differentiated cells like fibroblasts and vesicular cells do not show these memory mechanisms upon consecutive antigen exposure. Moreover, the pivotal role of Angiopoietin-like 4 (ANGPTL4) in regulating the memory functions of endometrial stem cells is identified through specific shRNA knockdown in vitro and knockout mice in vivo experiments. ANGPTL4 is associated with the alteration of diverse stem cell functions and epigenetic modifications, notably through histone H3 methylation changes and two pathways (i.e., PI3K/Akt and FAK/ERK1/2 signaling) upon consecutive antigen exposure. These findings imply the existence of inherent self-defense mechanisms through which local stem cells can adapt and protect themselves from recurrent antigenic challenges, ultimately mitigating adverse consequences.
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Affiliation(s)
- Se‐Ra Park
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
| | - Eun‐kyung Min
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
| | - Soo‐Rim Kim
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
| | - Suk‐Kyung Kim
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
| | - Kun‐Hee Na
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Microbiology, College of MedicineGachon UniversityIncheon21999Republic of Korea
| | - Chan Hum Park
- Department of Otolaryngology‐Head and Neck Surgery, Chuncheon Sacred Heart HospitalHallym University College of MedicineChuncheon24201Republic of Korea
| | - YunJae Jung
- Department of Microbiology, College of MedicineGachon UniversityIncheon21999Republic of Korea
| | - Byung‐Chul Oh
- Department of Physiology, Lee Gil Ya Cancer and Diabetes InstituteGachon University College of MedicineIncheon21999Republic of Korea
| | - In‐Sun Hong
- Department of Health Sciences and Technology, GAIHSTGachon UniversityIncheon21999Republic of Korea
- Department of Molecular Medicine, School of MedicineGachon UniversityIncheon406–840Republic of Korea
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3
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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [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: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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4
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Jakkamsetti V, Ma Q, Angulo G, Scudder W, Beutler B, Pascual JM. Genetic influences on motor learning and performance and superperforming mutants revealed by random mutational survey of the mouse genome. J Physiol 2024; 602:2649-2664. [PMID: 38299894 PMCID: PMC11142877 DOI: 10.1113/jp285505] [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: 08/21/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Evolution depends upon genetic variations that influence physiology. As defined in a genetic screen, phenotypic performance may be enhanced or degraded by such mutations. We set out to detect mutations that influence motor function, including motor learning. Thus, we tested the motor effects of 36,444 non-synonymous coding/splicing mutations induced in the germline of C57BL/6J mice with N-ethyl-N-nitrosourea by measuring changes in the performance of repetitive rotarod trials while blinded to genotype. Automated meiotic mapping was used to implicate individual mutations in causation. In total, 32,726 mice bearing all the variant alleles were screened. This was complemented with the simultaneous testing of 1408 normal mice for reference. In total, 16.3% of autosomal genes were thus rendered detectably hypomorphic or nullified by mutations in homozygosity and motor tested in at least three mice. This approach allowed us to identify superperformance mutations in Rif1, Tk1, Fan1 and Mn1. These genes are primarily related, among other less well-characterized functions, to nucleic acid biology. We also associated distinct motor learning patterns with groups of functionally related genes. These functional sets included, preferentially, histone H3 methyltransferase activity for mice that learnt at an accelerated rate relative to the remaining mutant mice. The results allow for an estimation of the fraction of mutations that can modify a behaviour influential for evolution such as locomotion. They may also enable, once the loci are further validated and the mechanisms elucidated, the harnessing of the activity of the newly identified genes to enhance motor ability or to counterbalance disability or disease. KEY POINTS: We studied the effect of chemically induced random mutations on mouse motor performance. An array of mutations influenced the rate of motor learning. DNA regulation genes predominated among these mutant loci. Several mutations in unsuspected genes led to superperformance. Assuming little-biased mutagenicity, the results allow for an estimation of the probability for any spontaneous mutation to influence a behaviour such as motor learning and ultimate performance.
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Affiliation(s)
- Vikram Jakkamsetti
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qian Ma
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gustavo Angulo
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - William Scudder
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Juan M. Pascual
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Eugene McDermott Center for Human Growth & Development / Center for Human Genetics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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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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6
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Coda DM, Gräff J. From cellular to fear memory: An epigenetic toolbox to remember. Curr Opin Neurobiol 2024; 84:102829. [PMID: 38128422 DOI: 10.1016/j.conb.2023.102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Throughout development, the neuronal epigenome is highly sensitive to external stimuli, yet capable of safeguarding cellular memory for a lifetime. In the adult brain, memories of fearful experiences are rapidly instantiated, yet can last for decades, but the mechanisms underlying such longevity remain unknown. Here, we showcase how fear memory formation and storage - traditionally thought to exclusively affect synapse-based events - elicit profound and enduring changes to the chromatin, proposing epigenetic regulation as a plausible molecular template for mnemonic processes. By comparing these to mechanisms occurring in development and differentiation, we notice that an epigenetic machinery similar to that preserving cellular memories might be employed by brain cells so as to form, store, and retrieve behavioral memories.
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Affiliation(s)
- Davide Martino Coda
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Federale Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Federale Lausanne (EPFL), 1015, Lausanne, Switzerland.
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Vitorakis N, Piperi C. Insights into the Role of Histone Methylation in Brain Aging and Potential Therapeutic Interventions. Int J Mol Sci 2023; 24:17339. [PMID: 38139167 PMCID: PMC10744334 DOI: 10.3390/ijms242417339] [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: 11/11/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Epigenetic mechanisms play a primary role in the cellular damage associated with brain aging. Histone posttranslational modifications represent intrinsic molecular alterations essential for proper physiological functioning, while divergent expression and activity have been detected in several aspects of brain aging. Aberrant histone methylation has been involved in neural stem cell (NSC) quiescence, microglial deficits, inflammatory processes, memory impairment, cognitive decline, neurodegenerative diseases, and schizophrenia. Herein, we provide an overview of recent studies on epigenetic regulation of brain tissue aging, mainly focusing on the role of histone methylation in different cellular and functional aspects of the aging process. Emerging targeting strategies of histone methylation are further explored, including neuroprotective drugs, natural compounds, and lifestyle modifications with therapeutic potential towards the aging process of the brain.
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Affiliation(s)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece;
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8
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Jakkamsetti V, Ma Q, Angulo G, Scudder W, Beutler B, Pascual JM. Genetic influences on motor learning and superperformance mutants revealed by random mutational survey of mouse locomotion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546756. [PMID: 37425744 PMCID: PMC10327015 DOI: 10.1101/2023.06.28.546756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Evolution depends upon genetic variations that influence physiology. As defined in a genetic screen, phenotypic performance may be enhanced or degraded by such mutations. We set out to detect mutations that influence motor function, including motor learning. Thus, we tested the motor effects of 36,444 non-synonymous coding/splicing mutations induced in the germline of C57BL/6J mice with N-ethyl-N-nitrosourea by measuring changes in the performance of repetitive rotarod trials while blinded to genotype. Automated meiotic mapping was used to implicate individual mutations in causation. 32,726 mice bearing all the variant alleles were screened. This was complemented with the simultaneous testing of 1,408 normal mice for reference. 16.3% of autosomal genes were thus rendered detectably hypomorphic or nullified by mutations in homozygosity and motor tested in at least 3 mice. This approach allowed us to identify superperformance mutations in Rif1, Tk1, Fan1 and Mn1. These genes are primarily related, among other less well characterized functions, to nucleic acid biology. We also associated distinct motor learning patterns with groups of functionally related genes. These functional sets included preferentially histone H3 methyltransferase activity for mice that learnt at an accelerated rate relative to the rest of mutant mice. The results allow for an estimation of the fraction of mutations that can modify a behavior influential for evolution such as locomotion. They may also enable, once the loci are further validated and the mechanisms elucidated, the harnessing of the activity of the newly identified genes to enhance motor ability or to counterbalance disability or disease.
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Affiliation(s)
- Vikram Jakkamsetti
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qian Ma
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gustavo Angulo
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - William Scudder
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Juan M. Pascual
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Eugene McDermott Center for Human Growth & Development / Center for Human Genetics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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10
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Abe K, Li J, Liu YY, Brent GA. Thyroid Hormone-mediated Histone Modification Protects Cortical Neurons From the Toxic Effects of Hypoxic Injury. J Endocr Soc 2022; 6:bvac139. [PMID: 36817622 PMCID: PMC9562813 DOI: 10.1210/jendso/bvac139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Indexed: 11/19/2022] Open
Abstract
Context Thyroid hormone has been shown to have a protective role in neuronal injury, although the mechanisms have not been established. The cellular response to stress that promotes adaptation and survival has been shown to involve epigenetic modifications. Objective We hypothesized that the neuroprotective role of thyroid hormone was associated with epigenetic modifications of histone proteins. We used hypoxic neurons as a model system for hypoxia-induced brain injury. Methods Mouse primary cortical neurons were exposed to 0.2% oxygen for 7 hours, with or without, treatment with triiodothyronine (T3). We analyzed the expression of histone-modifying enzymes by RNA-seq and the post-translationally modified histone 3 proteins by enzyme-linked immunosorbent assay (ELISA) and Western blot. Results We found that methylation of H3K27, associated with inactive promoters, was highly induced in hypoxic neurons, and this histone methylation was reduced by T3 treatment. H3K4 methylation is the hallmark of active promoters. The expression of 3 (Set1db, Kmta2c, and Kmt2e) out of 6 H3K4 methyltransferases was downregulated by hypoxia and expression was restored by T3 treatment. H3K4me3 protein, measured by ELISA, was increased 76% in T3-treated hypoxic neurons compared with the levels without T3 treatment. H3K56ac plays a critical role in transcription initiation and was markedly increased in T3-treated hypoxic neurons compared with those without T3 treatment, indicating stimulation of gene transcription. Additionally, T3 treatment restored hypoxia-induced downregulation of histone acetyltransferase, Kat6a, Kat6b, and Crebbp, which function as transcription factors. Conclusion These findings indicate that T3 treatment mitigates hypoxia-induced histone modifications and protects neurons from hypoxia-induced injury.
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Affiliation(s)
- Kiyomi Abe
- Division of Endocrinology, Diabetes and Metabolism, Departments of Medicine and Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA,Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Jianrong Li
- Division of Endocrinology, Diabetes and Metabolism, Departments of Medicine and Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA,Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA
| | - Yan Yun Liu
- Correspondence: Yan-Yun Liu, PhD, Division of Endocrinology, Diabetes and Metabolism, Departments of Medicine and Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA. ; or Gregory A. Brent, MD, Division of Endocrinology, Diabetes and Metabolism, Departments of Medicine and Physiology, David Geffen School of Medicine at UCLA, and Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA.
| | - Gregory A Brent
- Correspondence: Yan-Yun Liu, PhD, Division of Endocrinology, Diabetes and Metabolism, Departments of Medicine and Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA. ; or Gregory A. Brent, MD, Division of Endocrinology, Diabetes and Metabolism, Departments of Medicine and Physiology, David Geffen School of Medicine at UCLA, and Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA.
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11
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Belhocine M, Simonin M, Abad Flores JD, Cieslak A, Manosalva I, Pradel L, Smith C, Mathieu EL, Charbonnier G, Martens JHA, Stunnenberg HG, Maqbool MA, Mikulasova A, Russell LJ, Rico D, Puthier D, Ferrier P, Asnafi V, Spicuglia S. Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes. Genome Res 2022; 32:1328-1342. [PMID: 34162697 PMCID: PMC9341507 DOI: 10.1101/gr.266924.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 05/05/2021] [Indexed: 01/03/2023]
Abstract
Broad domains of H3K4 methylation have been associated with consistent expression of tissue-specific, cell identity, and tumor suppressor genes. Here, we identified broad domain-associated genes in healthy human thymic T cell populations and a collection of T cell acute lymphoblastic leukemia (T-ALL) primary samples and cell lines. We found that broad domains are highly dynamic throughout T cell differentiation, and their varying breadth allows the distinction between normal and neoplastic cells. Although broad domains preferentially associate with cell identity and tumor suppressor genes in normal thymocytes, they flag key oncogenes in T-ALL samples. Moreover, the expression of broad domain-associated genes, both coding and noncoding, is frequently deregulated in T-ALL. Using two distinct leukemic models, we showed that the ectopic expression of T-ALL oncogenic transcription factor preferentially impacts the expression of broad domain-associated genes in preleukemic cells. Finally, an H3K4me3 demethylase inhibitor differentially targets T-ALL cell lines depending on the extent and number of broad domains. Our results show that the regulation of broad H3K4me3 domains is associated with leukemogenesis, and suggest that the presence of these structures might be used for epigenetic prioritization of cancer-relevant genes, including long noncoding RNAs.
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Affiliation(s)
- Mohamed Belhocine
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
- Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates
| | - Mathieu Simonin
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - José David Abad Flores
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Agata Cieslak
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Iris Manosalva
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Lydie Pradel
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Charlotte Smith
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Eve-Lyne Mathieu
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Joost H A Martens
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculties of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, Netherlands
| | - Muhammad Ahmad Maqbool
- CRUK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Aderley Park, Macclesfield SK104TG, United Kingdom
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Lisa J Russell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Denis Puthier
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Pierre Ferrier
- Aix Marseille University, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, 13288 Marseille, France
| | - Vahid Asnafi
- Université de Paris (Descartes), Institut Necker-Enfants Malades (INEM), Institut national de la santé et de la recherche médicale (Inserm) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Hôpital Necker Enfants-Malades, 75015 Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, Theories and Approaches of Genomic Complexity (TAGC), UMR1090, 13288 Marseille, France
- Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
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12
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Histone macroH2A1 is a stronger regulator of hippocampal transcription and memory than macroH2A2 in mice. Commun Biol 2022; 5:482. [PMID: 35590030 PMCID: PMC9120515 DOI: 10.1038/s42003-022-03435-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/02/2022] [Indexed: 11/08/2022] Open
Abstract
Histone variants H2A.Z and H3.3 are epigenetic regulators of memory, but roles of other variants are not well characterized. macroH2A (mH2A) is a structurally unique histone that contains a globular macrodomain connected to the histone region by an unstructured linker. Here we assessed if mH2A regulates memory and if this role varies for the two mH2A-encoding genes, H2afy (mH2A1) and H2afy2 (mH2A2). We show that fear memory is impaired in mH2A1, but not in mH2A2-deficient mice, whereas both groups were impaired in a non-aversive spatial memory task. However, impairment was larger for mH2A1- deficient mice, indicating a preferential role for mH2A1 over mH2A2 in memory. Accordingly, mH2A1 depletion in the mouse hippocampus resulted in more extensive transcriptional de-repression compared to mH2A2 depletion. mH2A1-depleted mice failed to induce a normal transcriptional response to fear conditioning, suggesting that mH2A1 depletion impairs memory by altering transcription. Using chromatin immunoprecipitation (ChIP) sequencing, we found that both mH2A proteins are enriched on transcriptionally repressed genes, but only mH2A1 occupancy was dynamically modified during learning, displaying reduced occupancy on upregulated genes after training. These data identify mH2A as a regulator of memory and suggest that mH2A1 supports memory by repressing spurious transcription and promoting learning-induced transcriptional activation.
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13
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Michurina A, Sakib MS, Kerimoglu C, Krüger DM, Kaurani L, Islam MR, Joshi PD, Schröder S, Centeno TP, Zhou J, Pradhan R, Cha J, Xu X, Eichele G, Zeisberg EM, Kranz A, Stewart AF, Fischer A. Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes. EMBO J 2022; 41:e106459. [PMID: 34806773 PMCID: PMC8724770 DOI: 10.15252/embj.2020106459] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/04/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
In mammals, histone 3 lysine 4 methylation (H3K4me) is mediated by six different lysine methyltransferases. Among these enzymes, SETD1B (SET domain containing 1b) has been linked to syndromic intellectual disability in human subjects, but its role in the mammalian postnatal brain has not been studied yet. Here, we employ mice deficient for Setd1b in excitatory neurons of the postnatal forebrain, and combine neuron-specific ChIP-seq and RNA-seq approaches to elucidate its role in neuronal gene expression. We observe that Setd1b controls the expression of a set of genes with a broad H3K4me3 peak at their promoters, enriched for neuron-specific genes linked to learning and memory function. Comparative analyses in mice with conditional deletion of Kmt2a and Kmt2b histone methyltransferases show that SETD1B plays a more pronounced and potent role in regulating such genes. Moreover, postnatal loss of Setd1b leads to severe learning impairment, suggesting that SETD1B-dependent regulation of H3K4me levels in postnatal neurons is critical for cognitive function.
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Affiliation(s)
- Alexandra Michurina
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - M Sadman Sakib
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Cemil Kerimoglu
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Dennis Manfred Krüger
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Lalit Kaurani
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Md Rezaul Islam
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Parth Devesh Joshi
- Department for Gene and BehaviorMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Sophie Schröder
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Tonatiuh Pena Centeno
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Jiayin Zhou
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Ranjit Pradhan
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Julia Cha
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Xingbo Xu
- Department of Cardiology and PneumologyUniversity Medical Center of GöttingenGeorg‐August UniversityGöttingenGermany
- German Centre for Cardiovascular Research (DZHK)Partner Site GöttingenGöttingenGermany
| | - Gregor Eichele
- Department for Gene and BehaviorMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Elisabeth M Zeisberg
- Department of Cardiology and PneumologyUniversity Medical Center of GöttingenGeorg‐August UniversityGöttingenGermany
- German Centre for Cardiovascular Research (DZHK)Partner Site GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGermany
| | - Andrea Kranz
- Biotechnology CenterCenter for Molecular and Cellular BioengineeringDresden University of TechnologyDresdenGermany
| | - A Francis Stewart
- Biotechnology CenterCenter for Molecular and Cellular BioengineeringDresden University of TechnologyDresdenGermany
- Max‐Planck‐Institute for Cell Biology and GeneticsDresdenGermany
| | - André Fischer
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGermany
- Department of Psychiatry and PsychotherapyUniversity Medical Center GöttingenGöttingenGermany
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14
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Beacon TH, Delcuve GP, López C, Nardocci G, Kovalchuk I, van Wijnen AJ, Davie JR. The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes. Clin Epigenetics 2021; 13:138. [PMID: 34238359 PMCID: PMC8264473 DOI: 10.1186/s13148-021-01126-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted to narrow regions at the 5`end of the gene body, though a small subset of genes have a broad H3K4me3 domain which extensively covers the coding region. Although most studies focus on the H3K4me3 mark, the broad H3K4me3 domain is associated with a plethora of histone modifications (e.g., H3 acetylated at K27) and is therein termed broad epigenetic domain. Genes marked with the broad epigenetic domain are involved in cell identity and essential cell functions and have clinical potential as biomarkers for patient stratification. Reducing expression of genes with the broad epigenetic domain may increase the metastatic potential of cancer cells. Enhancers and super-enhancers interact with the broad epigenetic domain marked genes forming a hub of interactions involving nucleosome-depleted regions. Together, the regulatory elements coalesce with transcription factors, chromatin modifying/remodeling enzymes, coactivators, and the Mediator and/or Integrator complex into a transcription factory which may be analogous to a liquid–liquid phase-separated condensate. The broad epigenetic domain has a dynamic chromatin structure which supports frequent transcription bursts. In this review, we present the current knowledge of broad epigenetic domains.
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Affiliation(s)
- Tasnim H Beacon
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Geneviève P Delcuve
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Camila López
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada
| | - Gino Nardocci
- Faculty of Medicine, Universidad de Los Andes, Santiago, Chile.,Molecular Biology and Bioinformatics Lab, Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de Los Andes, Santiago, Chile
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - James R Davie
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, R3E 0V9, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Room 333A, Winnipeg, MB, Canada.
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15
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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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16
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Greer CB, Wright J, Weiss JD, Lazarenko RM, Moran SP, Zhu J, Chronister KS, Jin AY, Kennedy AJ, Sweatt JD, Kaas GA. Tet1 Isoforms Differentially Regulate Gene Expression, Synaptic Transmission, and Memory in the Mammalian Brain. J Neurosci 2021; 41:578-593. [PMID: 33262245 PMCID: PMC7842754 DOI: 10.1523/jneurosci.1821-20.2020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/28/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022] Open
Abstract
The dynamic regulation of DNA methylation in postmitotic neurons is necessary for memory formation and other adaptive behaviors. Ten-eleven translocation 1 (TET1) plays a part in these processes by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), thereby initiating active DNA demethylation. However, attempts to pinpoint its exact role in the nervous system have been hindered by contradictory findings, perhaps due in part, to a recent discovery that two isoforms of the Tet1 gene are differentially expressed from early development into adulthood. Here, we demonstrate that both the shorter transcript (Tet1S ) encoding an N-terminally truncated TET1 protein and a full-length Tet1 (Tet1FL ) transcript encoding canonical TET1 are co-expressed in the adult mouse brain. We show that Tet1S is the predominantly expressed isoform and is highly enriched in neurons, whereas Tet1FL is generally expressed at lower levels and more abundant in glia, suggesting their roles are at least partially cell type-specific. Using viral-mediated, isoform and neuron-specific molecular tools, we find that the individual repression of each transcript leads to the dysregulation of unique gene ensembles and contrasting changes in basal synaptic transmission. In addition, Tet1S repression enhances, while Tet1FL impairs, hippocampal-dependent memory in male mice. Together, our findings demonstrate that each Tet1 isoform serves a distinct role in the mammalian brain.SIGNIFICANCE STATEMENT In the brain, activity-dependent changes in gene expression are required for the formation of long-term memories. DNA methylation plays an essential role in orchestrating these learning-induced transcriptional programs by influencing chromatin accessibility and transcription factor binding. Once thought of as a stable epigenetic mark, DNA methylation is now known to be impermanent and dynamically regulated, driving neuroplasticity in the brain. We found that Tet1, a member of the ten-eleven translocation (TET) family of enzymes that mediates removal of DNA methyl marks, is expressed as two separate isoforms in the adult mouse brain and that each differentially regulates gene expression, synaptic transmission and memory formation. Together, our findings demonstrate that each Tet1 isoform serves a distinct role in the CNS.
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Affiliation(s)
- C B Greer
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - J Wright
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - J D Weiss
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - R M Lazarenko
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - S P Moran
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - J Zhu
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - K S Chronister
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - A Y Jin
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - A J Kennedy
- Department of Chemistry, Bates College, Lewiston, Maine 04240
| | - J D Sweatt
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
| | - G A Kaas
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
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17
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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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18
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Saw G, Tang FR. Epigenetic Regulation of the Hippocampus, with Special Reference to Radiation Exposure. Int J Mol Sci 2020; 21:ijms21249514. [PMID: 33327654 PMCID: PMC7765140 DOI: 10.3390/ijms21249514] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/12/2020] [Indexed: 01/28/2023] Open
Abstract
The hippocampus is crucial in learning, memory and emotion processing, and is involved in the development of different neurological and neuropsychological disorders. Several epigenetic factors, including DNA methylation, histone modifications and non-coding RNAs, have been shown to regulate the development and function of the hippocampus, and the alteration of epigenetic regulation may play important roles in the development of neurocognitive and neurodegenerative diseases. This review summarizes the epigenetic modifications of various cell types and processes within the hippocampus and their resulting effects on cognition, memory and overall hippocampal function. In addition, the effects of exposure to radiation that may induce a myriad of epigenetic changes in the hippocampus are reviewed. By assessing and evaluating the current literature, we hope to prompt a more thorough understanding of the molecular mechanisms that underlie radiation-induced epigenetic changes, an area which can be further explored.
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19
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Marogianni C, Georgouli D, Dadouli K, Ntellas P, Rikos D, Hadjigeorgiou GM, Spanaki C, Xiromerisiou G. Identification of a novel de novo KMT2B variant in a Greek dystonia patient via exome sequencing genotype-phenotype correlations of all published cases. Mol Biol Rep 2020; 48:371-379. [PMID: 33300088 DOI: 10.1007/s11033-020-06057-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/01/2020] [Indexed: 01/02/2023]
Abstract
Mutations in Lysine-Specific Histone Methyltransferase 2B gene (KMT2B) have been reported to be associated with isolated and complex early-onset generalized dystonia. We describe clinico-genetic features on a Greek patient with a novel de novo variant and demonstrate the phenotypic spectrum of KMT2B variants. We performed whole exome sequencing (WES), in a Greek patient with sporadic generalized dystonia. Additionally, we performed a systematic review of all published cases with KMT2B variants. The patient presented with isolated and mild generalized dystonia. We identified a novel splice site variant that was confirmed by Sanger sequencing and was not found in parents. This is the first reported KMT2B variant, in the Greek population. This case report further highlights the growing trend of identifying genetic diseases previously restricted to few cases in many different ethnic groups worldwide via exome sequencing. In the systematic review, we evaluated the mutation pathogenicity in all previously reported cases to investigate possible phenotype-genotype correlations. Greater mutation numbers in different populations will be important and mutation-specific functional studies will be essential to identify the pathogenicity of the various KMT2B variants.
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Affiliation(s)
- Chrysoula Marogianni
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - Despoina Georgouli
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - Katerina Dadouli
- Faculty of Medicine, Department of Hygiene and Epidemiology, University of Thessaly, Larissa, Greece
| | - Panagiotis Ntellas
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Dimitrios Rikos
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University Hospital of Larissa, University of Thessaly, Larissa, Greece
| | - Georgios M Hadjigeorgiou
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University Hospital of Larissa, University of Thessaly, Larissa, Greece.,Department of Neurology, Medical School, University of Cyprus, Nicosia, Cyprus
| | - Cleanthi Spanaki
- Department of Neurology, Medical School, University of Crete, Heraklion, Greece
| | - Georgia Xiromerisiou
- Department of Neurology, Faculty of Medicine, School of Health Sciences, University Hospital of Larissa, University of Thessaly, Larissa, Greece.
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20
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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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21
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Zovkic IB. Epigenetics and memory: an expanded role for chromatin dynamics. Curr Opin Neurobiol 2020; 67:58-65. [PMID: 32905876 DOI: 10.1016/j.conb.2020.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022]
Abstract
Nearly two decades of research on epigenetic mechanisms in the brain have demonstrated that epigenetic marks that were once thought to be relatively static are dynamically and reversibly regulated in the brain during memory formation. Here, we focus on new research that has further expanded the dynamic nature of chromatin in memory formation through three key mechanisms. First, we discuss the emerging role of histone variants, which undergo learning-induced turnover or exchange, a process in which one histone type replaces another in chromatin. Next, we focus on chromatin remodeling complexes, which are tightly intertwined with all aspects of chromatin regulation and as such, can reposition or evict nucleosomes to promote transcriptional induction, and mediate histone variant exchange. Finally, we discuss how differential distribution of histone marks to localized narrow genomic regions and/or broadly distributed chromatin domains impact transcriptional outcomes and memory formation. Together, these studies mark a shift toward unraveling the complexity of chromatin function in memory and offer new strategies for fine tuning transcriptional outcomes to modify longevity, specificity and strength of memories.
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Affiliation(s)
- Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Canada.
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Zhang C, Zuo Q, Wang M, Chen H, He N, Jin J, Li T, Jiang J, Yuan X, Li J, Shi X, Zhang M, Bai H, Zhang Y, Xu Q, Cui H, Chang G, Song J, Sun H, Zhang Y, Chen G, Li B. Narrow H3K4me2 is required for chicken PGC formation. J Cell Physiol 2020; 236:1391-1400. [PMID: 32749682 DOI: 10.1002/jcp.29945] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 01/12/2023]
Abstract
The development of primordial germ cells (PGCs) undergoes epigenetic modifications. The study of histone methylation in regulating PGCs is beneficial to understand the development and differentiation mechanism of germ stem cells. Notably, it provides a theoretical basis for directed induction and mass acquisition in vitro. However, little is known about the regulation of PGC formation by histone methylation. Here, we found the high enrichment of H3K4me2 in the blastoderm, genital ridges, and testis. Chromatin immunoprecipitation sequencing was performed and the results revealed that genomic H3K4me2 is dynamic in embryonic stem cells, PGCs, and spermatogonial stem cells. This trend was consistent with the H3K4me2 enrichment in the gene promoter region. Additionally, narrow region triggered PGC-related genes (Bmp4, Wnt5a, and Tcf7l2) and signaling pathways (Wnt and transforming growth factor-β). After knocking down histone methylase Mll2 in vitro and vivo, the level of H3K4me2 decreased, inhibiting Cvh and Blimp1 expression, then repressing the formation of PGCs. Taken together, our study revealed the whole genome map of H3K4me2 in the formation of PGCs, contributing to improve the epigenetic study in PGC formation and providing materials for bird gene editing and rescue of endangered birds.
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Affiliation(s)
- Chen Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qisheng Zuo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Man Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hao Chen
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Nana He
- Department of Experimental Medical Science, HwaMei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Jing Jin
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tingting Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingyi Jiang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xia Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiancheng Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiang Shi
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ming Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yang Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qi Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hengmi Cui
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, Maryland
| | - Hongyan Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yani Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Bichun Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Key Laboratory of Animal Breeding Reproduction and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Evaluation of sea cucumber peptides-assisted memory activity and acetylation modification in hippocampus of test mice based on scopolamine-induced experimental animal model of memory disorder. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.103909] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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24
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Park S, Kim GW, Kwon SH, Lee JS. Broad domains of histone H3 lysine 4 trimethylation in transcriptional regulation and disease. FEBS J 2020; 287:2891-2902. [PMID: 31967712 DOI: 10.1111/febs.15219] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/23/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022]
Abstract
Histone modifications affect transcription by changing the chromatin structure. In particular, histone H3 lysine 4 trimethylation (H3K4me3) is one of the most recognized epigenetic marks of active transcription. While many studies have provided evidence of the correlation between H3K4me3 and active transcription, details regarding the mechanism involved remain unclear. The first study on the broad H3K4me3 domain was reported in 2014; subsequently, the function of this domain has been studied in various cell types. In this review, we summarized the recent studies on the role of the broad H3K4me3 domain in transcription, development, memory formation, and several diseases, including cancer and autoimmune diseases. The broadest H3K4me3 domains are associated with increased transcriptional precision of cell-type-specific genes related to cell identity and other essential functions. The broad H3K4me3 domain regulates maternal zygotic activation in early mammalian development. In systemic autoimmune diseases, high expression of immune-responsive genes requires the presence of the broad H3K4me3 domain in the promoter-proximal regions. Transcriptional repression of tumor-suppressor genes is associated with the shortening of the broad H3K4me3 domains in cancer cells. Additionally, the broad H3K4me3 domain interacts with the super-enhancer to regulate cancer-associated genes. During memory formation, H3K4me3 breadth is regulated in the hippocampus CA1 neurons. Taken together, these findings indicate that H3K4me3 breadth is essential for the regulation of the transcriptional output across multiple cell types.
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Affiliation(s)
- Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, Korea
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