1
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Feierman ER, Louzon S, Prescott NA, Biaco T, Gao Q, Qiu Q, Choi K, Palozola KC, Voss AJ, Mehta SD, Quaye CN, Lynch KT, Fuccillo MV, Wu H, David Y, Korb E. Histone variant H2BE enhances chromatin accessibility in neurons to promote synaptic gene expression and long-term memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.575103. [PMID: 38352334 PMCID: PMC10862743 DOI: 10.1101/2024.01.29.575103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Regulation of histone proteins affects gene expression through multiple mechanisms including exchange with histone variants. However, widely expressed variants of H2B remain elusive. Recent findings link histone variants to neurological disorders, yet few are well studied in the brain. We applied new tools including novel antibodies, biochemical assays, and sequencing approaches to reveal broad expression of the H2B variant H2BE, and defined its role in regulating chromatin structure, neuronal transcription, and mouse behavior. We find that H2BE is enriched at promoters and a single unique amino acid allows it to dramatically enhance chromatin accessibility. Lastly, we show that H2BE is critical for synaptic gene expression and long-term memory. Together, these data reveal a novel mechanism linking histone variants to chromatin regulation, neuronal function, and memory. This work further identifies the first widely expressed H2B variant and uncovers a single histone amino acid with profound effects on genomic structure.
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Affiliation(s)
- Emily R. Feierman
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sean Louzon
- Cell and Molecular Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Nicholas A. Prescott
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Tracy Biaco
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Qingzeng Gao
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Kyuhyun Choi
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine C. Palozola
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Anna J. Voss
- Neuroscience Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Shreya D. Mehta
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Camille N. Quaye
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Katherine T. Lynch
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Marc V. Fuccillo
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-institutional PhD Program in Chemical Biology, New York, NY
| | - Erica Korb
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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2
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Kim RK, Truby NL, Silva GM, Picone JA, Miller CS, Baldwin AN, Neve RL, Cui X, Hamilton PJ. Histone H1x in mouse ventral hippocampus associates with, but does not cause behavioral adaptations to stress. Transl Psychiatry 2024; 14:239. [PMID: 38834575 PMCID: PMC11150540 DOI: 10.1038/s41398-024-02931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024] Open
Abstract
Prior research has identified differential protein expression levels of linker histone H1x within the ventral hippocampus (vHipp) of stress-susceptible versus stress-resilient mice. These mice are behaviorally classified based on their divergent responses to chronic social stress. Here, we sought to determine whether elevated vHipp H1x protein levels directly contribute to these diverging behavioral adaptations to stress. First, we demonstrated that stress-susceptible mice uniquely express elevated vHipp H1x protein levels following chronic stress. Given that linker histones coordinate heterochromatin compaction, we hypothesize that elevated levels of H1x in the vHipp may impede pro-resilience transcriptional adaptations and prevent development of the resilient phenotype following social stress. To test this, 8-10-week-old male C57BL/6 J mice were randomly assigned to groups undergoing 10 days of chronic social defeat stress (CSDS) or single housing, respectively. Following CSDS, mice were classified as susceptible versus resilient based on their social interaction behaviors. We synthesized a viral overexpression (OE) vector for H1x and transduced all stressed and single housed mice with either H1x or control GFP within vHipp. Following viral delivery, we conducted social, anxiety-like, and memory-reliant behavior tests on distinct cohorts of mice. We found no behavioral adaptations following H1x OE compared to GFP controls in susceptible, resilient, or single housed mice. In sum, although we confirm elevated vHipp protein levels of H1x associate with susceptibility to social stress, we observe no significant behavioral consequence of H1x OE. Thus, we conclude elevated levels of H1x are associated with, but are not singularly sufficient to drive development of behavioral adaptations to stress.
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Affiliation(s)
- R Kijoon Kim
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Natalie L Truby
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Gabriella M Silva
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Joseph A Picone
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Cary S Miller
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Amber N Baldwin
- Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Rachael L Neve
- Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, MA, USA
| | - Xiaohong Cui
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Peter J Hamilton
- Department of Anatomy and Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA.
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3
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Paniri A, Hosseini MM, Akhavan-Niaki H. Alzheimer's Disease-Related Epigenetic Changes: Novel Therapeutic Targets. Mol Neurobiol 2024; 61:1282-1317. [PMID: 37700216 DOI: 10.1007/s12035-023-03626-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Aging is a significant risk factor for Alzheimer's disease (AD), although the precise mechanism and molecular basis of AD are not yet fully understood. Epigenetic mechanisms, such as DNA methylation and hydroxymethylation, mitochondrial DNA methylation, histone modifications, and non-coding RNAs (ncRNAs), play a role in regulating gene expression related to neuron plasticity and integrity, which are closely associated with learning and memory development. This review describes the impact of dynamic and reversible epigenetic modifications and factors on memory and plasticity throughout life, emphasizing their potential as target for therapeutic intervention in AD. Additionally, we present insight from postmortem and animal studies on abnormal epigenetics regulation in AD, as well as current strategies aiming at targeting these factors in the context of AD therapy.
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Affiliation(s)
- Alireza Paniri
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran
| | | | - Haleh Akhavan-Niaki
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran.
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4
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Reda A, Hategan LA, McLean TAB, Creighton SD, Luo JQ, Chen SES, Hua S, Winston S, Reeves I, Padmanabhan A, Dahi TA, Ramzan F, Brimble MA, Murphy PJ, Walters BJ, Stefanelli G, Zovkic IB. Role of the histone variant H2A.Z.1 in memory, transcription, and alternative splicing is mediated by lysine modification. Neuropsychopharmacology 2024:10.1038/s41386-024-01817-2. [PMID: 38366138 DOI: 10.1038/s41386-024-01817-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Creating long-lasting memories requires learning-induced changes in gene expression, which are impacted by epigenetic modifications of DNA and associated histone proteins. Post-translational modifications (PTMs) of histones are key regulators of transcription, with different PTMs producing unique effects on gene activity and behavior. Although recent studies implicate histone variants as novel regulators of memory, effects of PTMs on the function of histone variants are rarely considered. We previously showed that the histone variant H2A.Z suppresses memory, but it is unclear if this role is impacted by H2A.Z acetylation, a PTM that is typically associated with positive effects on transcription and memory. To answer this question, we used a mutation approach to manipulate acetylation on H2A.Z without impacting acetylation of other histone types. Specifically, we used adeno-associated virus (AAV) constructs to overexpress mutated H2A.Z.1 isoforms that either mimic acetylation (acetyl-mimic) by replacing lysines 4, 7 and 11 with glutamine (KQ), or H2A.Z.1 with impaired acetylation (acetyl-defective) by replacing the same lysines with alanine (KA). Expressing the H2A.Z.1 acetyl-mimic (H2A.Z.1KQ) improved memory under weak learning conditions, whereas expressing the acetyl-defective H2A.Z.1KA generally impaired memory, indicating that the effect of H2A.Z.1 on memory depends on its acetylation status. RNA sequencing showed that H2A.Z.1KQ and H2A.Z.1KA uniquely impact the expression of different classes of genes in both females and males. Specifically, H2A.Z.1KA preferentially impacts genes involved in synaptic function, suggesting that acetyl-defective H2A.Z.1 impairs memory by altering synaptic regulation. Finally, we describe, for the first time, that H2A.Z is also involved in alternative splicing of neuronal genes, whereby H2A.Z depletion, as well as expression of H2A.Z.1 lysine mutants influence transcription and splicing of different gene targets, suggesting that H2A.Z.1 can impact behavior through effects on both splicing and gene expression. This is the first study to demonstrate that direct manipulation of H2A.Z post-translational modifications regulates memory, whereby acetylation adds another regulatory layer by which histone variants can fine tune higher brain functions through effects on gene expression and splicing.
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Affiliation(s)
- Anas Reda
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Luca A Hategan
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Timothy A B McLean
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Samantha D Creighton
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Jian Qi Luo
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Sean En Si Chen
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3G3, Canada
| | - Shan Hua
- Departments of Biology and Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Stephen Winston
- Department of Surgery and Graduate school of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Isaiah Reeves
- Department of Surgery and Graduate school of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Aditya Padmanabhan
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Tarkan A Dahi
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Firyal Ramzan
- Department of Biology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Mark A Brimble
- Department of Host-Microbe Interactions, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Patrick J Murphy
- Departments of Biology and Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Brandon J Walters
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada
| | - Gilda Stefanelli
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
| | - Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada.
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5
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Kim RK, Truby NL, Silva GM, Picone JA, Miller CS, Neve RL, Cui X, Hamilton PJ. Histone H1x in mouse ventral hippocampus correlates with, but does not cause behavioral adaptations to stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.06.565881. [PMID: 37986938 PMCID: PMC10659322 DOI: 10.1101/2023.11.06.565881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Prior research has identified differential protein expression levels of linker histone H1x within the ventral hippocampus (vHipp) of stress-susceptible versus stress-resilient mice. These mice are behaviorally classified based on their divergent responses to chronic social stress. Here, we sought to determine whether elevated vHipp H1x protein levels directly contribute to these diverging behavioral adaptations to stress. First, we demonstrate that stress-susceptible mice uniquely express elevated vHipp H1x protein levels following chronic stress. Given that linker histones coordinate heterochromatin compaction, we hypothesize that elevated levels of H1x in the vHipp may impede pro-resilience transcriptional adaptations and prevent development of the resilient phenotype following social stress. To test this, 8-10-week-old male C57BL/6J mice were randomly assigned to stressed and unstressed groups undergoing 10 days of chronic social defeat stress (CSDS) or single housing respectively. Following CSDS, mice were classified as susceptible versus resilient based on their social interaction behaviors. We synthesized a viral overexpression (OE) vector for H1x and transduced experimental mice with either H1x or control GFP within vHipp. Following viral delivery, we conducted social, anxiety-like, and memory-reliant behavior tests on distinct cohorts of mice. We found no behavioral adaptations following H1x OE compared to GFP controls in susceptible, resilient, or unstressed mice. In sum, although we confirm vHipp protein levels of H1x correlate with susceptibility to social stress, we observe no significant behavioral consequence of H1x OE. Thus, we conclude elevated levels of H1x are correlated with, but are not singularly sufficient to drive development of behavioral adaptations to stress.
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6
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Wang Q, Qi Y, Xiong F, Wang D, Wang B, Chen Y. The H2A.Z-KDM1A complex promotes tumorigenesis by localizing in the nucleus to promote SFRP1 promoter methylation in cholangiocarcinoma cells. BMC Cancer 2022; 22:1166. [PMID: 36368958 PMCID: PMC9652970 DOI: 10.1186/s12885-022-10279-y] [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: 06/27/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background Intrahepatic cholangiocarcinoma (ICC), originating from the bile ducts, is the second most common primary liver malignancy, and its incidence has recently increased. H2A.Z, a highly conserved H2A variant, is emerging as a key regulatory molecule in cancer. However, its underlying mechanism of action in ICC cells remains unclear. Methods Here, we examined the expression of H2A.Z and SFRP1 in normal intrahepatic cholangiocytes, ICC cell lines, ICC tissue microarrays, and fresh specimens. The correlations between H2A.Z or SFRP1 expression and clinical features were analysed. The overall survival rate was analysed based on H2A.Z and SFRP1 expression. Immunoprecipitation was used to analyse the recruitment of KDM1A, and ChIP sequencing and BSP were used to analyse the enrichment of methylation-related molecules such as H3K4me1 and H3K4me2 in the SFRP1 promoter and reveal the underlying mechanisms. Knockdown and rescue experiments were used to determine the potential mechanism by which H2A.Z and SFRP1 promote tumorigenesis in vitro. Results We showed that upregulation of H2A.Z expression is linked to downregulation of SFRP1 expression in ICC tissues and poor overall survival in patients with ICC. H2A.Z interacted with KDM1A in the nucleus to bind to the -151 ~ -136 bp region upstream of the SFRP1 promoter to increase its demethylation in ICC cells. Functionally, H2A.Z silencing inhibited the proliferation and invasion of ICC cells, and these effects were mitigated by SFRP1 silencing in ICC cells. Conclusions Our findings reveal that H2A.Z inhibits SFRP1 expression through chromatin modification in the context of ICC by forming a complex with KDM1A in the nucleus. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10279-y.
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Feng Y, Zhang Y, Lin Z, Ye X, Lin X, Lv L, Lin Y, Sun S, Qi Y, Lin X. Chromatin remodeler Dmp18 regulates apoptosis by controlling H2Av incorporation in Drosophila imaginal disc development. PLoS Genet 2022; 18:e1010395. [PMID: 36166470 PMCID: PMC9514664 DOI: 10.1371/journal.pgen.1010395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Programmed Cell Death (PCD) or apoptosis is a highly conserved biological process and plays essential roles both in the development and stress context. In Drosophila, expression of pro-apoptotic genes, including reaper (rpr), head involution defective (hid), grim, and sickle (skl), is sufficient to induce cell death. Here, we demonstrate that the chromatin remodeler Dmp18, the homolog of mammalian Znhit1, plays a crucial role in regulating apoptosis in eye and wing development. We showed that loss of Dmp18 disrupted eye and wing development, up-regulated transcription of pro-apoptotic genes, and induced apoptosis. Inhibition of apoptosis suppressed the eye defects caused by Dmp18 deletion. Furthermore, loss of Dmp18 disrupted H2Av incorporation into chromatin, promoted H3K4me3, but reduced H3K27me3 modifications on the TSS regions of pro-apoptotic genes. These results indicate that Dmp18 negatively regulates apoptosis by mediating H2Av incorporation and histone H3 modifications at pro-apoptotic gene loci for transcriptional regulation. Our study uncovers the role of Dmp18 in regulating apoptosis in Drosophila eye and wing development and provides insights into chromatin remodeling regulating apoptosis at the epigenetic levels.
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Affiliation(s)
- Ying Feng
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- * E-mail: (YF); (YQ); (XL)
| | - Yan Zhang
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhiqing Lin
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaolei Ye
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xue Lin
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lixiu Lv
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Lin
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shenfei Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (YF); (YQ); (XL)
| | - Xinhua Lin
- State Key Laboratory of Optometry, Ophthalmology and Vision Science, School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Greater Bay Area Institute of Precision Medicine (Guangzhou), Zhongshan Hospital, Fudan University, Shanghai, China
- * E-mail: (YF); (YQ); (XL)
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8
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Kreienbaum C, Paasche LW, Hake SB. H2A.Z's 'social' network: functional partners of an enigmatic histone variant. Trends Biochem Sci 2022; 47:909-920. [PMID: 35606214 DOI: 10.1016/j.tibs.2022.04.014] [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: 02/15/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
Abstract
The histone variant H2A.Z has been extensively studied to understand its manifold DNA-based functions. In the past years, researchers identified its specific binding partners, the 'H2A.Z interactome', that convey H2A.Z-dependent chromatin changes. Here, we summarize the latest findings regarding vertebrate H2A.Z-associated factors and focus on their roles in gene activation and repression, cell cycle regulation, (neuro)development, and tumorigenesis. Additionally, we demonstrate how protein-protein interactions and post-translational histone modifications can fine-tune the complex interplay of H2A.Z-regulated gene expression. Last, we review the most recent results on interactors of the two isoforms H2A.Z.1 and H2A.Z.2.1, which differ in only three amino acids, and focus on cancer-associated mutations of H2A and H2A.Z, which reveal fascinating insights into the functional importance of such minuscule changes.
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Affiliation(s)
| | - Lena W Paasche
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany.
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9
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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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10
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Herchenröther A, Wunderlich TM, Lan J, Hake SB. Spotlight on histone H2A variants: From B to X to Z. Semin Cell Dev Biol 2022; 135:3-12. [PMID: 35365397 DOI: 10.1016/j.semcdb.2022.03.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/18/2022] [Accepted: 03/20/2022] [Indexed: 12/30/2022]
Abstract
Chromatin, the functional organization of DNA with histone proteins in eukaryotic nuclei, is the tightly-regulated template for several biological processes, such as transcription, replication, DNA damage repair, chromosome stability and sister chromatid segregation. In order to achieve a reversible control of local chromatin structure and DNA accessibility, various interconnected mechanisms have evolved. One of such processes includes the deposition of functionally-diverse variants of histone proteins into nucleosomes, the building blocks of chromatin. Among core histones, the family of H2A histone variants exhibits the largest number of members and highest sequence-divergence. In this short review, we report and discuss recent discoveries concerning the biological functions of the animal histone variants H2A.B, H2A.X and H2A.Z and how dysregulation or mutation of the latter impacts the development of disease.
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Affiliation(s)
| | - Tim M Wunderlich
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany
| | - Jie Lan
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus Liebig University, 35390 Giessen, Germany.
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11
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What makes a histone variant a variant: Changing H2A to become H2A.Z. PLoS Genet 2021; 17:e1009950. [PMID: 34871303 PMCID: PMC8675926 DOI: 10.1371/journal.pgen.1009950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 12/16/2021] [Accepted: 11/16/2021] [Indexed: 01/01/2023] Open
Abstract
Chromatin structure and underlying DNA accessibility is modulated by the incorporation of histone variants. H2A.Z, a variant of the H2A core histone family, plays a distinct and essential role in a diverse set of biological functions including gene regulation and maintenance of heterochromatin-euchromatin boundaries. Although it is currently unclear how the replacement of H2A with H2A.Z can regulate gene expression, the variance in their amino acid sequence likely contributes to their functional differences. To tease apart regions of H2A.Z that confer its unique identity, a set of plasmids expressing H2A-H2A.Z hybrids from the native H2A.Z promoter were examined for their ability to recapitulate H2A.Z function. First, we found that the H2A.Z M6 region was necessary and sufficient for interaction with the SWR1-C chromatin remodeler. Remarkably, the combination of only 9 amino acid changes, the H2A.Z M6 region, K79 and L81 (two amino acids in the α2-helix), were sufficient to fully rescue growth phenotypes of the htz1Δ mutant. Furthermore, combining three unique H2A.Z regions (K79 and L81, M6, C-terminal tail) was sufficient for expression of H2A.Z-dependent heterochromatin-proximal genes and GAL1 derepression. Surprisingly, hybrid constructs that restored the transcription of H2A.Z-dependent genes, did not fully recapitulate patterns of H2A.Z-specific enrichment at the tested loci. This suggested that H2A.Z function in transcription regulation may be at least partially independent of its specific localization in chromatin. Together, this work has identified three regions that can confer specific H2A.Z-identity to replicative H2A, furthering our understanding of what makes a histone variant a variant. Chromatin structure in eukaryotes is integral to all aspects of genome function. Many essential biological processes depend on chromatin remodeling for regulating access to DNA such as transcription, replication, and DNA repair. One highly conserved method of chromatin remodeling is the replacement of the replicative histones with a histone variant. Unlike replicative histones, which are distributed equally in chromatin during DNA replication, histone variants can be transcribed and deposited throughout the cell cycle at specific locations. Once incorporated, small differences in a histone variant’s protein sequence and structure can result in unique chromatin neighbourhoods with distinct character and function from the replicative histone. Therefore, to better understand the role of a histone variant, it is important to define how its protein sequence contributes to its unique identity. Here, using a hybrid gene approach in budding yeast, we systematically determine which amino acids contribute to H2A.Z unique identity as a histone variant.
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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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Colino-Sanguino Y, Clark SJ, Valdes-Mora F. The H2A.Z-nuclesome code in mammals: emerging functions. Trends Genet 2021; 38:273-289. [PMID: 34702577 DOI: 10.1016/j.tig.2021.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022]
Abstract
H2A.Z is a histone variant that provides specific structural and docking-side properties to the nucleosome, resulting in diverse and specialised molecular and cellular functions. In this review, we discuss the latest studies uncovering new functional aspects of mammalian H2A.Z in gene transcription, including pausing and elongation of RNA polymerase II (RNAPII) and enhancer activity; DNA repair; DNA replication; and 3D chromatin structure. We also review the recently described role of H2A.Z in embryonic development, cell differentiation, neurodevelopment, and brain function. In conclusion, our cumulative knowledge of H2A.Z over the past 40 years, in combination with the implementation of novel molecular technologies, is unravelling an unexpected and complex role of histone variants in gene regulation and disease.
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Affiliation(s)
- Yolanda Colino-Sanguino
- Cancer Epigenetics Biology and Therapeutics, Precision Medicine Theme, Children's Cancer Institute, Sydney, NSW, Australia; School of Children and Women Health, University of NSW Sydney, Sydney, NSW, Australia.
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Fatima Valdes-Mora
- Cancer Epigenetics Biology and Therapeutics, Precision Medicine Theme, Children's Cancer Institute, Sydney, NSW, Australia; School of Children and Women Health, University of NSW Sydney, Sydney, NSW, Australia.
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Cameron B, Lehrmann E, Chih T, Walters J, Buksch R, Snyder S, Goffena J, Lefcort F, Becker KG, George L. Loss of Elp1 perturbs histone H2A.Z and the Notch signaling pathway. Biol Open 2021; 10:272332. [PMID: 34590699 PMCID: PMC8496692 DOI: 10.1242/bio.058979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022] Open
Abstract
Elongator dysfunction is increasingly recognized as a contributor to multiple neurodevelopmental and neurodegenerative disorders including familial dysautonomia, intellectual disability, amyotrophic lateral sclerosis, and autism spectrum disorder. Although numerous cellular processes are perturbed in the context of Elongator loss, converging evidence from multiple studies has resolved Elongator's primary function in the cell to the modification of tRNA wobble uridines and the translational regulation of codon-biased genes. Here we characterize H2a.z, encoding the variant H2a histone H2A.Z, as an indirect Elongator target. We further show that canonical Notch signaling, a pathway directed by H2A.Z, is perturbed as a consequence of Elp1 loss. Finally, we demonstrate that hyperacetylation of H2A.Z and other histones via exposure to the histone deacetylase inhibitor Trichostatin A during neurogenesis corrects the expression of Notch3 and rescues the development of sensory neurons in embryos lacking the Elp1 Elongator subunit. Summary: The maldevelopment of sensory neurons in Elongator knockout embryos is associated with elevated H2A.Z and perturbed Notch signaling that can be rescued by Trichostatin A.
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Affiliation(s)
- BreAnna Cameron
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Elin Lehrmann
- Computational Biology & Genomics Core (CBGC), Laboratory of Genetics and Genomics (LGG), Department of Health and Human Services (DHHS), National Institute on Aging, Intramural Research Program (NIA IRP), National Institutes of Health (NIH), Biomedical Research Center, Baltimore, MD 21224, USA
| | - Tien Chih
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Joseph Walters
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Richard Buksch
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Sara Snyder
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Joy Goffena
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Frances Lefcort
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Lynn George
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
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15
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Lowden C, Boulet A, Boehler NA, Seecharran S, Rios Garcia J, Lowe NJ, Liu J, Ong JLK, Wang W, Ma L, Cheng AH, Senatore A, Monks DA, Liu BH, Leary SC, Cheng HYM. Homeostatic control of nuclear-encoded mitochondrial gene expression by the histone variant H2A.Z is essential for neuronal survival. Cell Rep 2021; 36:109704. [PMID: 34525369 DOI: 10.1016/j.celrep.2021.109704] [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: 06/05/2020] [Revised: 06/22/2021] [Accepted: 08/20/2021] [Indexed: 11/16/2022] Open
Abstract
Histone variants are crucial regulators of chromatin structure and gene transcription, yet their functions within the brain remain largely unexplored. Here, we show that the H2A histone variant H2A.Z is essential for neuronal survival. Mice lacking H2A.Z in GABAergic neurons or Purkinje cells (PCs) present with a progressive cerebellar ataxia accompanied by widespread degeneration of PCs. Ablation of H2A.Z in other neuronal subtypes also triggers cell death. H2A.Z binds to the promoters of key nuclear-encoded mitochondrial genes to regulate their expression and promote organelle function. Bolstering mitochondrial activity genetically or by organelle transplant enhances the survival of H2A.Z-ablated neurons. Changes in bioenergetic status alter H2A.Z occupancy at the promoters of nuclear-encoded mitochondrial genes, an adaptive response essential for cell survival. Our results highlight that H2A.Z fulfills a key, conserved role in neuronal survival by acting as a transcriptional rheostat to regulate the expression of genes critical to mitochondrial function.
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Affiliation(s)
- Christopher Lowden
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Aren Boulet
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Nicholas A Boehler
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Shavanie Seecharran
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Julian Rios Garcia
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Nicholas J Lowe
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Jiashu Liu
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Jonathan L K Ong
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Wanzhang Wang
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Lingfeng Ma
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Arthur H Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Adriano Senatore
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - D Ashley Monks
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada; Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Bao-Hua Liu
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Scot C Leary
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada.
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16
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Stefanelli G, Makowski CE, Brimble MA, Hall M, Reda A, Creighton SD, Leonetti AM, McLean TAB, Zakaria JM, Baumbach J, Greer CB, Davidoff AM, Walters BJ, Murphy PJ, Zovkic IB. The histone chaperone Anp32e regulates memory formation, transcription, and dendritic morphology by regulating steady-state H2A.Z binding in neurons. Cell Rep 2021; 36:109551. [PMID: 34407406 PMCID: PMC8422973 DOI: 10.1016/j.celrep.2021.109551] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 06/08/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Rapid removal of histone H2A.Z from neuronal chromatin is a key step in learning-induced gene expression and memory formation, but mechanisms underlying learning-induced H2A.Z removal are unclear. Anp32e was recently identified as an H2A.Z-specific histone chaperone that removes H2A.Z from nucleosomes in dividing cells, but its role in non-dividing neurons is unclear. Moreover, prior studies investigated Anp32e function under steady-state rather than stimulus-induced conditions. Here, we show that Anp32e regulates H2A.Z binding in neurons under steady-state conditions, with lesser impact on stimulus-induced H2A.Z removal. Functionally, Anp32e depletion leads to H2A.Z-dependent impairment in transcription and dendritic arborization in cultured hippocampal neurons, as well as impaired recall of contextual fear memory and transcriptional regulation. Together, these data indicate that Anp32e regulates behavioral and morphological outcomes by preventing H2A.Z accumulation in chromatin rather than by regulating activity-mediated H2A.Z dynamics.
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Affiliation(s)
- Gilda Stefanelli
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Claire E Makowski
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mark A Brimble
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Meaghan Hall
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Anas Reda
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Samantha D Creighton
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Amanda M Leonetti
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Timothy A B McLean
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Jacqueline M Zakaria
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Jennet Baumbach
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Celeste B Greer
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brandon J Walters
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA.
| | - Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G3, Canada.
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JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions. Int J Mol Sci 2021; 22:ijms22020678. [PMID: 33445503 PMCID: PMC7826843 DOI: 10.3390/ijms22020678] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 12/22/2022] Open
Abstract
Histone variants differ in amino acid sequence, expression timing and genomic localization sites from canonical histones and convey unique functions to eukaryotic cells. Their tightly controlled spatial and temporal deposition into specific chromatin regions is accomplished by dedicated chaperone and/or remodeling complexes. While quantitatively identifying the chaperone complexes of many human H2A variants by using mass spectrometry, we also found additional members of the known H2A.Z chaperone complexes p400/TIP60/NuA4 and SRCAP. We discovered JAZF1, a nuclear/nucleolar protein, as a member of a p400 sub-complex containing MBTD1 but excluding ANP32E. Depletion of JAZF1 results in transcriptome changes that affect, among other pathways, ribosome biogenesis. To identify the underlying molecular mechanism contributing to JAZF1's function in gene regulation, we performed genome-wide ChIP-seq analyses. Interestingly, depletion of JAZF1 leads to reduced H2A.Z acetylation levels at > 1000 regulatory sites without affecting H2A.Z nucleosome positioning. Since JAZF1 associates with the histone acetyltransferase TIP60, whose depletion causes a correlated H2A.Z deacetylation of several JAZF1-targeted enhancer regions, we speculate that JAZF1 acts as chromatin modulator by recruiting TIP60's enzymatic activity. Altogether, this study uncovers JAZF1 as a member of a TIP60-containing p400 chaperone complex orchestrating H2A.Z acetylation at regulatory regions controlling the expression of genes, many of which are involved in ribosome biogenesis.
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18
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Li Z, Rasmussen LJ. TIP60 in aging and neurodegeneration. Ageing Res Rev 2020; 64:101195. [PMID: 33091598 DOI: 10.1016/j.arr.2020.101195] [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: 08/04/2020] [Revised: 09/29/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023]
Abstract
Epigenetic modification of chromatin, including histone methylation and acetylation, plays critical roles in eukaryotic cells and has a significant impact on chromatin structure/accessibility, gene regulation and, susceptibility to aging, neurodegenerative disease, cancer, and other age-related diseases. This article reviews the current advances on TIP60/KAT5, a major histone acetyltransferase with diverse functions in eukaryotes, with emphasis on its regulation of autophagy, proteasome-dependent protein turnover, RNA transcription, DNA repair, circadian rhythms, learning and memory, and other neurological functions implicated in aging and neurodegeneration. Moreover, the promising therapeutic potential of TIP60 is discussed to target Alzheimer's disease and other neurological diseases.
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19
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An Emerging Role of m6A in Memory: A Case for Translational Priming. Int J Mol Sci 2020; 21:ijms21207447. [PMID: 33050279 PMCID: PMC7589748 DOI: 10.3390/ijms21207447] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/30/2022] Open
Abstract
Investigation into the role of methylation of the adenosine base (m6A) of RNA has only recently begun, but it quickly became apparent that m6A is able to control and fine-tune many aspects of mRNA, from splicing to translation. The ability of m6A to regulate translation distally, away from traditional sites near the nucleus, quickly caught the eye of neuroscientists because of implications for selective protein translation at synapses. Work in the brain has demonstrated how m6A is functionally required for many neuronal functions, but two in particular are covered at length here: The role of m6A in 1) neuron development; and 2) memory formation. The purpose of this review is not to cover all data about m6A in the brain. Instead, this review will focus on connecting mechanisms of m6A function in neuron development, with m6A’s known function in memory formation. We will introduce the concept of “translational priming” and discuss how current data fit into this model, then speculate how m6A-mediated translational priming during memory consolidation can regulate learning and memory locally at the synapse.
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20
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Zhang M, Zhao J, Lv Y, Wang W, Feng C, Zou W, Su L, Jiao J. Histone Variants and Histone Modifications in Neurogenesis. Trends Cell Biol 2020; 30:869-880. [PMID: 33011018 DOI: 10.1016/j.tcb.2020.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/20/2022]
Abstract
During embryonic brain development, neurogenesis requires the orchestration of gene expression to regulate neural stem cell (NSC) fate specification. Epigenetic regulation with specific emphasis on the modes of histone variants and histone post-translational modifications are involved in interactive gene regulation of central nervous system (CNS) development. Here, we provide a broad overview of the regulatory system of histone variants and histone modifications that have been linked to neurogenesis and diseases. We also review the crosstalk between different histone modifications and discuss how the 3D genome affects cell fate dynamics during brain development. Understanding the mechanisms of epigenetic regulation in neurogenesis has shifted the paradigm from single gene regulation to synergistic interactions to ensure healthy embryonic neurogenesis.
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Affiliation(s)
- Mengtian Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyue Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqing Lv
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenwen Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Sciences, University of Science and Technology of China, Hefei 230000, China
| | - Chao Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenzheng Zou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libo Su
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Innovation Academy for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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21
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Creighton SD, Stefanelli G, Reda A, Zovkic IB. Epigenetic Mechanisms of Learning and Memory: Implications for Aging. Int J Mol Sci 2020; 21:E6918. [PMID: 32967185 PMCID: PMC7554829 DOI: 10.3390/ijms21186918] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
The neuronal epigenome is highly sensitive to external events and its function is vital for producing stable behavioral outcomes, such as the formation of long-lasting memories. The importance of epigenetic regulation in memory is now well established and growing evidence points to altered epigenome function in the aging brain as a contributing factor to age-related memory decline. In this review, we first summarize the typical role of epigenetic factors in memory processing in a healthy young brain, then discuss the aspects of this system that are altered with aging. There is general agreement that many epigenetic marks are modified with aging, but there are still substantial inconsistencies in the precise nature of these changes and their link with memory decline. Here, we discuss the potential source of age-related changes in the epigenome and their implications for therapeutic intervention in age-related cognitive decline.
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Affiliation(s)
- Samantha D. Creighton
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
| | - Gilda Stefanelli
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
| | - Anas Reda
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada;
| | - Iva B. Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada; (S.D.C.); (G.S.)
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S, Canada;
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22
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Ramzan F, Baumbach J, Monks AD, Zovkic IB. Histone H2A.Z is required for androgen receptor-mediated effects on fear memory. Neurobiol Learn Mem 2020; 175:107311. [PMID: 32916283 DOI: 10.1016/j.nlm.2020.107311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/13/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic factors translate environmental signals into stable outcomes, but how they are influenced by regulators of plasticity remain unclear. We previously showed that androgen receptor overexpression inhibited fear memory in male mice and increased expression of the histone variant H2A.Z, a novel epigenetic regulator of memory. Here, we used conditional-inducible H2A.Z knockout mice to investigate how H2A.Z deletion influences androgenic regulation of fear memory. We showed that conditional inducible H2A.Z deletion blocked memory-enhancing effects of androgen depletion (induced by gonadectomy), and of pharmacological inhibition of the androgen receptor with flutamide. Similarly, H2A.Z deletion blocked the memory-reducing effects of DHT, and DHT treatment in cultured hippocampal neurons altered H2A.Z binding, suggesting that AR is an H2A.Z regulator in neurons. Overall, these data show that fear memory formation is regulated by interactions between sex hormones and epigenetic factors, which has implications for sex differences in fear-related disorders.
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Affiliation(s)
- Firyal Ramzan
- University of Toronto Mississauga, Department of Psychology, Mississauga, Ontario L5L 1C6, Canada
| | - Jennet Baumbach
- University of Toronto Mississauga, Department of Psychology, Mississauga, Ontario L5L 1C6, Canada
| | - Ashley D Monks
- University of Toronto Mississauga, Department of Psychology, Mississauga, Ontario L5L 1C6, Canada
| | - Iva B Zovkic
- University of Toronto Mississauga, Department of Psychology, Mississauga, Ontario L5L 1C6, Canada.
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23
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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: 8] [Impact Index Per Article: 2.0] [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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24
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Sex-specific effects of the histone variant H2A.Z on fear memory, stress-enhanced fear learning and hypersensitivity to pain. Sci Rep 2020; 10:14331. [PMID: 32868857 PMCID: PMC7458907 DOI: 10.1038/s41598-020-71229-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/12/2020] [Indexed: 01/01/2023] Open
Abstract
Emerging evidence suggests that histone variants are novel epigenetic regulators of memory, whereby histone H2A.Z suppresses fear memory. However, it is not clear if altered fear memory can also modify risk for PTSD, and whether these effects differ in males and females. Using conditional-inducible H2A.Z knockout (cKO) mice, we showed that H2A.Z binding is higher in females and that H2A.Z cKO enhanced fear memory only in males. However, H2A.Z cKO improved memory on the non-aversive object-in-place task in both sexes, suggesting that H2A.Z suppresses non-stressful memory irrespective of sex. Given that risk for fear-related disorders, such as PTSD, is biased toward females, we examined whether H2A.Z cKO also has sex-specific effects on fear sensitization in the stress-enhanced fear learning (SEFL) model of PTSD, as well as associated changes in pain sensitivity. We found that H2A.Z cKO reduced stress-induced sensitization of fear learning and pain responses preferentially in female mice, indicating that the effects of H2A.Z depend on sex and the type of task, and are influenced by history of stress. These data suggest that H2A.Z may be a sex-specific epigenetic risk factor for PTSD susceptibility, with implications for developing sex-specific therapeutic interventions.
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25
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Pierre A, Van Schuerbeek A, Allaoui W, Van Laere S, Singewald N, Van Eeckhaut A, Smolders I, De Bundel D. Effects of ghrelin receptor activation on forebrain dopamine release, conditioned fear and fear extinction in C57BL/6J mice. J Neurochem 2020; 154:389-403. [DOI: 10.1111/jnc.14996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Anouk Pierre
- Department of Pharmaceutical Sciences Research Group Experimental Pharmacology Center for Neurosciences (C4N) Vrije Universiteit Brussel Brussels Belgium
| | - Andries Van Schuerbeek
- Department of Pharmaceutical Sciences Research Group Experimental Pharmacology Center for Neurosciences (C4N) Vrije Universiteit Brussel Brussels Belgium
| | - Wissal Allaoui
- Department of Pharmaceutical Sciences Research Group Experimental Pharmacology Center for Neurosciences (C4N) Vrije Universiteit Brussel Brussels Belgium
| | - Sven Van Laere
- Interfaculty Center Data Processing & Statistics Vrije Universiteit Brussel Brussels Belgium
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology Institute of Pharmacy and CMBI University of Innsbruck Innsbruck Austria
| | - Ann Van Eeckhaut
- Department of Pharmaceutical Sciences Research Group Experimental Pharmacology Center for Neurosciences (C4N) Vrije Universiteit Brussel Brussels Belgium
| | - Ilse Smolders
- Department of Pharmaceutical Sciences Research Group Experimental Pharmacology Center for Neurosciences (C4N) Vrije Universiteit Brussel Brussels Belgium
| | - Dimitri De Bundel
- Department of Pharmaceutical Sciences Research Group Experimental Pharmacology Center for Neurosciences (C4N) Vrije Universiteit Brussel Brussels Belgium
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26
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Colino-Sanguino Y, Cornett EM, Moulder D, Smith GC, Hrit J, Cordeiro-Spinetti E, Vaughan RM, Krajewski K, Rothbart SB, Clark SJ, Valdés-Mora F. A Read/Write Mechanism Connects p300 Bromodomain Function to H2A.Z Acetylation. iScience 2019; 21:773-788. [PMID: 31727574 PMCID: PMC6889796 DOI: 10.1016/j.isci.2019.10.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 09/20/2019] [Accepted: 10/24/2019] [Indexed: 12/22/2022] Open
Abstract
Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active regulatory regions associated with gene expression. Although the Tip60 complex is proposed to acetylate H2A.Z, functional studies suggest additional enzymes are involved. Here, we show that p300 acetylates H2A.Z at multiple lysines. In contrast, we found that although Tip60 does not efficiently acetylate H2A.Z in vitro, genetic inhibition of Tip60 reduces H2A.Zac in cells. Importantly, we found that interaction between the p300-bromodomain and H4 acetylation (H4ac) enhances p300-driven H2A.Zac. Indeed, H2A.Zac and H4ac show high genomic overlap, especially at active promoters. We also reveal unique chromatin features and transcriptional states at enhancers correlating with co-occurrence or exclusivity of H4ac and H2A.Zac. We propose that differential H4 and H2A.Z acetylation signatures can also define the enhancer state. In conclusion, we show both Tip60 and p300 contribute to H2A.Zac and reveal molecular mechanisms of writer/reader crosstalk between H2A.Z and H4 acetylation through p300. p300 acetylates H2A.Z at multiple N-terminal lysine residues Interaction of p300 bromodomain with H4ac enhances H2A.Zac H2A.Zac and H4ac co-localize at active regulatory regions H4ac and H2A.Zac differential signature can define the enhancer state
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Affiliation(s)
- Yolanda Colino-Sanguino
- Histone Variants Group, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David Moulder
- Histone Variants Group, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Grady C Smith
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Joel Hrit
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Robert M Vaughan
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia.
| | - Fátima Valdés-Mora
- Histone Variants Group, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia.
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27
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Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
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Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
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28
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Herre M, Korb E. The chromatin landscape of neuronal plasticity. Curr Opin Neurobiol 2019; 59:79-86. [PMID: 31174107 DOI: 10.1016/j.conb.2019.04.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/18/2019] [Indexed: 01/27/2023]
Abstract
Examining the links between neuronal activity, transcriptional output, and synaptic function offers unique insights into how neurons adapt to changing environments and form memories. Epigenetic markers, such as DNA methylation and histone modifications, have been implicated in the formation of not only cellular memories such as cell fate, but also memories of experience at the organismal level. Here, we review recent advances in chromatin regulation that contribute to synaptic plasticity and drive adaptive behaviors through dynamic and precise regulation of transcription output in neurons. We discuss chromatin-associated proteins, histone variant proteins, the contribution of cis-regulatory elements and their interaction with histone modifications, and how these mechanisms are integrated into distinct behavior and environmental response paradigms.
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Affiliation(s)
- Margaret Herre
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Erica Korb
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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