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Spencer PS, Valdes Angues R, Edridge AWD, Palmer VS, Boele van Hensbroek M. Response to Prof. Robert Colebunders' Letter submitted to JNS regarding: Spencer PS, Valdes Angues R, Palmer VS. Nodding syndrome: A role for environmental biotoxins that dysregulate MECP2 expression? J Neurol Sci. 2024 Jul 15;462:123077. doi: 10.1016/j.jns.2024.123077. J Neurol Sci 2024; 463:123153. [PMID: 39117466 DOI: 10.1016/j.jns.2024.123153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024]
Affiliation(s)
- Peter S Spencer
- Department of Neurology, School of Medicine, and Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR, USA.
| | - Raquel Valdes Angues
- Department of Neurology, School of Medicine, Oregon Health & Science University, Portland, OR, USA.
| | - Arthur W D Edridge
- Amsterdam Centre for Global Child Health, Emma Children's Hospital, Amsterdam UMC, Location University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.
| | - Valerie S Palmer
- Department of Neurology, School of Medicine, Oregon Health & Science University, Portland, OR, USA.
| | - Michael Boele van Hensbroek
- Amsterdam Centre for Global Child Health, Emma Children's Hospital, Amsterdam UMC, Location University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
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Battista S, Fedele M, Secco L, Ingo AMD, Sgarra R, Manfioletti G. Binding to the Other Side: The AT-Hook DNA-Binding Domain Allows Nuclear Factors to Exploit the DNA Minor Groove. Int J Mol Sci 2024; 25:8863. [PMID: 39201549 PMCID: PMC11354804 DOI: 10.3390/ijms25168863] [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: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
The "AT-hook" is a peculiar DNA-binding domain that interacts with DNA in the minor groove in correspondence to AT-rich sequences. This domain has been first described in the HMGA protein family of architectural factors and later in various transcription factors and chromatin proteins, often in association with major groove DNA-binding domains. In this review, using a literature search, we identified about one hundred AT-hook-containing proteins, mainly chromatin proteins and transcription factors. After considering the prototypes of AT-hook-containing proteins, the HMGA family, we review those that have been studied in more detail and that have been involved in various pathologies with a particular focus on cancer. This review shows that the AT-hook is a domain that gives proteins not only the ability to interact with DNA but also with RNA and proteins. This domain can have enzymatic activity and can influence the activity of the major groove DNA-binding domain and chromatin docking modules when present, and its activity can be modulated by post-translational modifications. Future research on the function of AT-hook-containing proteins will allow us to better decipher their function and contribution to the different pathologies and to eventually uncover their mutual influences.
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Affiliation(s)
- Sabrina Battista
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Monica Fedele
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Luca Secco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | - Guidalberto Manfioletti
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
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3
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Kalani L, Kim BH, de Chavez AR, Roemer A, Mikhailov A, Merritt JK, Good KV, Chow RL, Delaney KR, Hendzel MJ, Zhou Z, Neul JL, Vincent JB, Ausió J. Testing the PEST hypothesis using relevant Rett mutations in MeCP2 E1 and E2 isoforms. Hum Mol Genet 2024:ddae119. [PMID: 39137370 DOI: 10.1093/hmg/ddae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/19/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Mutations in methyl-CpG binding protein 2 (MeCP2), such as the T158M, P152R, R294X, and R306C mutations, are responsible for most Rett syndrome (RTT) cases. These mutations often result in altered protein expression that appears to correlate with changes in the nuclear size; however, the molecular details of these observations are poorly understood. Using a C2C12 cellular system expressing human MeCP2-E1 isoform as well as mouse models expressing these mutations, we show that T158M and P152R result in a decrease in MeCP2 protein, whereas R306C has a milder variation, and R294X resulted in an overall 2.5 to 3 fold increase. We also explored the potential involvement of the MeCP2 PEST domains in the proteasome-mediated regulation of MeCP2. Finally, we used the R294X mutant to gain further insight into the controversial competition between MeCP2 and histone H1 in the chromatin context. Interestingly, in R294X, MeCP2 E1 and E2 isoforms were differently affected, where the E1 isoform contributes to much of the overall protein increase observed, while E2 decreases by half. The modes of MeCP2 regulation, thus, appear to be differently regulated in the two isoforms.
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Affiliation(s)
- Ladan Kalani
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - Alberto Ruiz de Chavez
- Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - Anastasia Roemer
- Departments of Oncology and Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Ave, Edmonton, AB T6G 2H7, Canada
| | - Anna Mikhailov
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St, Toronto, ON M5T 1R8, Canada
| | - Jonathan K Merritt
- Vanderbilt Kennedy Center, Departments of Pediatrics, Pharmacology, and Special Education, Vanderbilt University Medical Center and Vanderbilt University, 1211 Medical Center Dr, Nashville, TN 37232, United States
| | - Katrina V Good
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St, Toronto, ON M5T 1R8, Canada
| | - Robert L Chow
- Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - Kerry R Delaney
- Department of Biology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
| | - Michael J Hendzel
- Departments of Oncology and Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Ave, Edmonton, AB T6G 2H7, Canada
| | - Zhaolan Zhou
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, 3400 Civic Center Blvd, Philadelphia, PA 19104, United States
| | - Jeffrey L Neul
- Vanderbilt Kennedy Center, Departments of Pediatrics, Pharmacology, and Special Education, Vanderbilt University Medical Center and Vanderbilt University, 1211 Medical Center Dr, Nashville, TN 37232, United States
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 250 College St, Toronto, ON M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, 27 King's College Cir, Toronto, ON M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, 27 King College Cir, Toronto, ON M5T 1R8, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, 3800 Finnerty Rd, Victoria, BC V8W 2Y2, Canada
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4
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Maurici N, Phan TM, Henty-Ridilla JL, Kim YC, Mittal J, Bah A. Uncovering the molecular interactions underlying MBD2 and MBD3 phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591564. [PMID: 38746378 PMCID: PMC11092444 DOI: 10.1101/2024.04.29.591564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Chromatin organization controls DNA's accessibility to regulatory factors to influence gene expression. Heterochromatin, or transcriptionally silent chromatin enriched in methylated DNA and methylated histone tails, self-assembles through multivalent interactions with its associated proteins into a condensed, but dynamic state. Liquid-liquid phase separation (LLPS) of key heterochromatin regulators, such as heterochromatin protein 1 (HP1), plays an essential role in heterochromatin assembly and function. Methyl-CpG-binding protein 2 (MeCP2), the most studied member of the methyl-CpG-binding domain (MBD) family of proteins, has been recently shown to undergo LLPS in the absence and presence of methylated DNA. These studies provide a new mechanistic framework for understanding the role of methylated DNA and its readers in heterochromatin formation. However, the details of the molecular interactions by which other MBD family members undergo LLPS to mediate genome organization and transcriptional regulation are not fully understood. Here, we focus on two MBD proteins, MBD2 and MBD3, that have distinct but interdependent roles in gene regulation. Using an integrated computational and experimental approach, we uncover the homotypic and heterotypic interactions governing MBD2 and MBD3 phase separation and DNA's influence on this process. We show that despite sharing the highest sequence identity and structural homology among all the MBD protein family members, MBD2 and MBD3 exhibit differing residue patterns resulting in distinct phase separation mechanisms. Understanding the molecular underpinnings of MBD protein condensation offers insights into the higher-order, LLPS-mediated organization of heterochromatin.
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Schmidt A, Zhang H, Schmitt S, Rausch C, Popp O, Chen J, Cmarko D, Butter F, Dittmar G, Lermyte F, Cardoso MC. The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues. Cells 2024; 13:139. [PMID: 38247831 PMCID: PMC10814525 DOI: 10.3390/cells13020139] [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: 11/01/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions from these tissues, analyzed their protein compositions using quantitative mass spectrometry, and compared them to identify common and tissue-specific PCH proteins. In addition to heterochromatin-enriched proteins, the PCH proteome includes RNA/transcription and membrane-related proteins, which showed lower abundance than PCH-enriched proteins. Thus, we applied a cut-off of PCH-unspecific candidates based on their abundance and validated PCH-enriched proteins. Amongst the hits, MeCP2 was classified into brain PCH-enriched proteins, while linker histone H1 was not. We found that H1 and MeCP2 compete to bind to PCH and regulate PCH organization in opposite ways. Altogether, our workflow of unbiased PCH isolation, quantitative mass spectrometry, and validation-based analysis allowed the identification of proteins that are common and tissue-specifically enriched at PCH. Further investigation of selected hits revealed their opposing role in heterochromatin higher-order architecture in vivo.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Stephanie Schmitt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Oliver Popp
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Jiaxuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dusan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gunnar Dittmar
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Frederik Lermyte
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
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6
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Rastegar M, Davie JR. MeCP2 is the protector of epigenome integrity, membrane-less nuclear architecture, and stability of chromatin assembly. Epigenomics 2023; 15:1027-1031. [PMID: 37937403 DOI: 10.2217/epi-2023-0310] [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] [Indexed: 11/09/2023] Open
Abstract
Tweetable abstract MeCP2 is an epigenetic factor with global impact in epigenome integrity, membrane-less nuclear architecture, and chromatin stability. Our Editorial covers recent advances on these important topics.
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Affiliation(s)
- Mojgan Rastegar
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, R3E 0J9, Canada
| | - James R Davie
- Department of Biochemistry & Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, R3E 0J9, Canada
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7
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Smolen P, Dash PK, Redell JB. Traumatic brain injury-associated epigenetic changes and the risk for neurodegenerative diseases. Front Neurosci 2023; 17:1259405. [PMID: 37795186 PMCID: PMC10546067 DOI: 10.3389/fnins.2023.1259405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Epidemiological studies have shown that traumatic brain injury (TBI) increases the risk for developing neurodegenerative diseases (NDs). However, molecular mechanisms that underlie this risk are largely unidentified. TBI triggers widespread epigenetic modifications. Similarly, NDs such as Alzheimer's or Parkinson's are associated with numerous epigenetic changes. Although epigenetic changes can persist after TBI, it is unresolved if these modifications increase the risk of later ND development and/or dementia. We briefly review TBI-related epigenetic changes, and point out putative feedback loops that might contribute to long-term persistence of some modifications. We then focus on evidence suggesting persistent TBI-associated epigenetic changes may contribute to pathological processes (e.g., neuroinflammation) which may facilitate the development of specific NDs - Alzheimer's disease, Parkinson's disease, or chronic traumatic encephalopathy. Finally, we discuss possible directions for TBI therapies that may help prevent or delay development of NDs.
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Affiliation(s)
- Paul Smolen
- Department of Neurobiology and Anatomy, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
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8
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Rueter J, Rimbach G, Huebbe P. Allelic variation within the major APOE CpG island affects its methylation in the brain of targeted replacement mice expressing human APOE. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194942. [PMID: 37196888 DOI: 10.1016/j.bbagrm.2023.194942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Affiliation(s)
- Johanna Rueter
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, D-24118 Kiel, Germany
| | - Gerald Rimbach
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, D-24118 Kiel, Germany.
| | - Patricia Huebbe
- Institute of Human Nutrition and Food Science, University of Kiel, Hermann-Rodewald-Strasse 6, D-24118 Kiel, Germany
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9
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Liang J, Xin C, Xin M, Wang G, Wu X. An insertion mutation of the MECP2 gene in severe neonatal encephalopathy and ocular and oropharyngeal dyskinesia: a case report. BMC Med Genomics 2023; 16:181. [PMID: 37537631 PMCID: PMC10398912 DOI: 10.1186/s12920-023-01616-6] [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: 01/08/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Pathogenic variation of the MECP2 gene presents mostly as Rett syndrome in females and is extremely rare in males. Most male patients with MECP2 gene mutation show MECP2 duplication syndrome. CASE PRESENTATION Here we report a rare case in a 10-month-old boy with a hemizygous insertion mutation in MECP2 as NM_001110792, c.799_c.800insAGGAAGC, which results in a frameshift mutation (p.R267fs*6). The patient presented with severe encephalopathy in the neonatal period, accompanied by severe development backwardness, hypotonia, and ocular and oropharyngeal dyskinesia. This is the first report of this mutation, which highlights the phenotype variability associated with MECP2 variants. CONCLUSIONS This case helps to expand the clinical spectrum associated with MECP2 variants. Close attention should be paid to the growth and development of patients carrying a MECP2 variant or Xq28 duplication. Early interventions may help improve symptoms to some certain extent.
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Affiliation(s)
- Jianmin Liang
- Department of Pediatric, Neurology of Jilin University, 1 Xinmin Street, Changchun, 130000, Jilin Province, China
- Jilin Provincial Key Laboratory of Pediatric Neurology, Changchun, China
| | - Cuijuan Xin
- Department of Pediatric, Neurology of Jilin University, 1 Xinmin Street, Changchun, 130000, Jilin Province, China
| | - Meiying Xin
- Department of Pediatric, Neurology of Jilin University, 1 Xinmin Street, Changchun, 130000, Jilin Province, China
| | - Guangliang Wang
- Department of Cardiology, Jiren Hospital of Far Eastern Horizon, Anda, China
| | - Xuemei Wu
- Department of Pediatric, Neurology of Jilin University, 1 Xinmin Street, Changchun, 130000, Jilin Province, China.
- Jilin Provincial Key Laboratory of Pediatric Neurology, Changchun, China.
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Idris M, Coussement L, Alves MM, De Meyer T, Melotte V. Promoter hypermethylation of neural-related genes is compatible with stemness in solid cancers. Epigenetics Chromatin 2023; 16:31. [PMID: 37537688 PMCID: PMC10398991 DOI: 10.1186/s13072-023-00505-7] [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: 05/31/2023] [Accepted: 07/22/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND DNA hypermethylation is an epigenetic feature that modulates gene expression, and its deregulation is observed in cancer. Previously, we identified a neural-related DNA hypermethylation fingerprint in colon cancer, where most of the top hypermethylated and downregulated genes have known functions in the nervous system. To evaluate the presence of this signature and its relevance to carcinogenesis in general, we considered 16 solid cancer types available in The Cancer Genome Atlas (TCGA). RESULTS All tested cancers showed significant enrichment for neural-related genes amongst hypermethylated genes. This signature was already present in two premalignant tissue types and could not be explained by potential confounders such as bivalency status or tumor purity. Further characterization of the neural-related DNA hypermethylation signature in colon cancer showed particular enrichment for genes that are overexpressed during neural differentiation. Lastly, an analysis of upstream regulators identified RE1-Silencing Transcription factor (REST) as a potential mediator of this DNA methylation signature. CONCLUSION Our study confirms the presence of a neural-related DNA hypermethylation fingerprint in various cancers, of genes linked to neural differentiation, and points to REST as a possible regulator of this mechanism. We propose that this fingerprint indicates an involvement of DNA hypermethylation in the preservation of neural stemness in cancer cells.
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Affiliation(s)
- Musa Idris
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6229 HX, Maastricht, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children's Hospital, 3015 GD, Rotterdam, The Netherlands
| | - Louis Coussement
- Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Maria M Alves
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children's Hospital, 3015 GD, Rotterdam, The Netherlands
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, 9000, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000, Ghent, Belgium
| | - Veerle Melotte
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, P.O. Box 616, 6229 HX, Maastricht, The Netherlands.
- Department of Clinical Genetics, Erasmus University Medical Center-Sophia Children's Hospital, 3015 GD, Rotterdam, The Netherlands.
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11
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Porter RS, Iwase S. Modulation of chromatin architecture influences the neuronal nucleus through activity-regulated gene expression. Biochem Soc Trans 2023; 51:703-713. [PMID: 36929379 PMCID: PMC10959270 DOI: 10.1042/bst20220889] [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: 11/25/2022] [Revised: 02/02/2023] [Accepted: 02/22/2023] [Indexed: 03/18/2023]
Abstract
The disruption of chromatin-regulating genes is associated with many neurocognitive syndromes. While most of these genes are ubiquitously expressed across various cell-types, many chromatin regulators act upon activity regulated genes (ARGs) that play central roles in synaptic development and plasticity. Recent literature suggests a link between ARG expression disruption in neurons with the human phenotypes observed in various neurocognitive syndromes. Advances in chromatin biology have demonstrated how chromatin structure, from nucleosome occupancy to higher-order structures such as topologically associated domains, impacts the kinetics of transcription. This review discusses the dynamics of these various levels of chromatin structure and their influence on the expression of ARGs.
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Affiliation(s)
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
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12
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Giuliani A, Sabbatinelli J, Amatori S, Graciotti L, Silvestrini A, Matacchione G, Ramini D, Mensà E, Prattichizzo F, Babini L, Mattiucci D, Busilacchi EM, Bacalini MG, Espinosa E, Lattanzio F, Procopio AD, Olivieri F, Poloni A, Fanelli M, Rippo MR. MiR-422a promotes adipogenesis via MeCP2 downregulation in human bone marrow mesenchymal stem cells. Cell Mol Life Sci 2023; 80:75. [PMID: 36847916 PMCID: PMC9971129 DOI: 10.1007/s00018-023-04719-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 12/16/2022] [Accepted: 01/22/2023] [Indexed: 03/01/2023]
Abstract
Methyl-CpG binding protein 2 (MeCP2) is a ubiquitous transcriptional regulator. The study of this protein has been mainly focused on the central nervous system because alterations of its expression are associated with neurological disorders such as Rett syndrome. However, young patients with Rett syndrome also suffer from osteoporosis, suggesting a role of MeCP2 in the differentiation of human bone marrow mesenchymal stromal cells (hBMSCs), the precursors of osteoblasts and adipocytes. Here, we report an in vitro downregulation of MeCP2 in hBMSCs undergoing adipogenic differentiation (AD) and in adipocytes of human and rat bone marrow tissue samples. This modulation does not depend on MeCP2 DNA methylation nor on mRNA levels but on differentially expressed miRNAs during AD. MiRNA profiling revealed that miR-422a and miR-483-5p are upregulated in hBMSC-derived adipocytes compared to their precursors. MiR-483-5p, but not miR-422a, is also up-regulated in hBMSC-derived osteoblasts, suggesting a specific role of the latter in the adipogenic process. Experimental modulation of intracellular levels of miR-422a and miR-483-5p affected MeCP2 expression through direct interaction with its 3' UTR elements, and the adipogenic process. Accordingly, the knockdown of MeCP2 in hBMSCs through MeCP2-targeting shRNA lentiviral vectors increased the levels of adipogenesis-related genes. Finally, since adipocytes released a higher amount of miR-422a in culture medium compared to hBMSCs we analyzed the levels of circulating miR-422a in patients with osteoporosis-a condition characterized by increased marrow adiposity-demonstrating that its levels are negatively correlated with T- and Z-scores. Overall, our findings suggest that miR-422a has a role in hBMSC adipogenesis by downregulating MeCP2 and its circulating levels are associated with bone mass loss in primary osteoporosis.
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Affiliation(s)
- Angelica Giuliani
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy.
| | - Jacopo Sabbatinelli
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy.,SOD Medicina di Laboratorio, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Stefano Amatori
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Fano, PU, Italy
| | - Laura Graciotti
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy.,Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Silvestrini
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy
| | - Giulia Matacchione
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy
| | - Deborah Ramini
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy
| | | | - Lucia Babini
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy
| | - Domenico Mattiucci
- Section of Hematology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Elena Marinelli Busilacchi
- Section of Hematology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Giulia Bacalini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Laboratorio Brain Aging, Bologna, Italy
| | - Emma Espinosa
- Geriatrics, Santa Croce Hospital, Azienda Ospedaliera Ospedali Riuniti Marche Nord, Fano, Italy
| | | | - Antonio Domenico Procopio
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy.,Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy.,Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
| | - Antonella Poloni
- Section of Hematology, Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, Molecular Pathology Laboratory "PaoLa", University of Urbino Carlo Bo, Fano, PU, Italy
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy.
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13
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Panayotis N, Ehinger Y, Felix MS, Roux JC. State-of-the-art therapies for Rett syndrome. Dev Med Child Neurol 2023; 65:162-170. [PMID: 36056801 PMCID: PMC10087176 DOI: 10.1111/dmcn.15383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023]
Abstract
Rett syndrome (RTT) is an X-linked neurogenetic disorder caused by mutations of the MECP2 (methyl-CpG-binding protein 2) gene. Over two decades of work established MeCP2 as a protein with pivotal roles in the regulation of the epigenome, neuronal physiology, synaptic maintenance, and behaviour. Given the genetic aetiology of RTT and the proof of concept of its reversal in a mouse model, considerable efforts have been made to design therapeutic approaches to re-express MeCP2. By being at the forefront of the development of innovative gene therapies, research on RTT is of paramount importance for the treatment of monogenic neurological diseases. Here we discuss the recent advances and challenges of promising genetic strategies for the treatment of RTT including gene replacement therapies, gene/RNA editing strategies, and reactivation of the silenced X chromosome. WHAT THIS PAPER ADDS: Recent advances shed light on the promises of gene replacement therapy with new vectors designed to control the levels of MeCP2 expression. New developments in DNA/RNA editing approaches or reactivation of the silenced X chromosome open the possibility to re-express the native MeCP2 locus at endogenous levels. Current strategies still face limitations in transduction efficiency and future work is needed to improve brain delivery.
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Affiliation(s)
- Nicolas Panayotis
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.,Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.,Université Paris Cité, CNRS, Saints-Pères Paris Institute for the Neurosciences, Paris, France
| | - Yann Ehinger
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
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14
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Jarczak J, Miszczak M, Radwanska K. Is DNA methylation in the brain a mechanism of alcohol use disorder? Front Behav Neurosci 2023; 17:957203. [PMID: 36778133 PMCID: PMC9908583 DOI: 10.3389/fnbeh.2023.957203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Alcohol use disorder (AUD) is a worldwide problem. Unfortunately, the molecular mechanisms of alcohol misuse are still poorly understood, therefore successful therapeutic approaches are limited. Accumulating data indicate that the tendency for compulsive alcohol use is inherited, suggesting a genetic background as an important factor. However, the probability to develop AUD is also affected by life experience and environmental factors. Therefore, the epigenetic modifications that are altered over lifetime likely contribute to increased risk of alcohol misuse. Here, we review the literature looking for the link between DNA methylation in the brain, a common epigenetic modification, and AUD-related behaviors in humans, mice and rats. We sum up the main findings, identify the existing gaps in our knowledge and indicate future directions of the research.
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15
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Schmidt A, Frei J, Poetsch A, Chittka A, Zhang H, Aßmann C, Lehmkuhl A, Bauer UM, Nuber UA, Cardoso MC. MeCP2 heterochromatin organization is modulated by arginine methylation and serine phosphorylation. Front Cell Dev Biol 2022; 10:941493. [PMID: 36172281 PMCID: PMC9510713 DOI: 10.3389/fcell.2022.941493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Rett syndrome is a human intellectual disability disorder that is associated with mutations in the X-linked MECP2 gene. The epigenetic reader MeCP2 binds to methylated cytosines on the DNA and regulates chromatin organization. We have shown previously that MECP2 Rett syndrome missense mutations are impaired in chromatin binding and heterochromatin reorganization. Here, we performed a proteomics analysis of post-translational modifications of MeCP2 isolated from adult mouse brain. We show that MeCP2 carries various post-translational modifications, among them phosphorylation on S80 and S421, which lead to minor changes in either heterochromatin binding kinetics or clustering. We found that MeCP2 is (di)methylated on several arginines and that this modification alters heterochromatin organization. Interestingly, we identified the Rett syndrome mutation site R106 as a dimethylation site. In addition, co-expression of protein arginine methyltransferases (PRMT)1 and PRMT6 lead to a decrease of heterochromatin clustering. Altogether, we identified and validated novel modifications of MeCP2 in the brain and show that these can modulate its ability to bind as well as reorganize heterochromatin, which may play a role in the pathology of Rett syndrome.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jana Frei
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Ansgar Poetsch
- Queen Mary School, Medical College, Nanchang University, Nanchang, China
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Alexandra Chittka
- Division of Medicine, The Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Chris Aßmann
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
| | - Ulrike A. Nuber
- Stem Cell and Developmental Biology, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
- *Correspondence: Ulrike A. Nuber, ; M. Cristina Cardoso,
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16
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Zhang H, Romero H, Schmidt A, Gagova K, Qin W, Bertulat B, Lehmkuhl A, Milden M, Eck M, Meckel T, Leonhardt H, Cardoso MC. MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation. Nucleus 2022; 13:1-34. [PMID: 35156529 PMCID: PMC8855868 DOI: 10.1080/19491034.2021.2024691] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Hui Zhang
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Hector Romero
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Annika Schmidt
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Katalina Gagova
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Weihua Qin
- Faculty of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Bianca Bertulat
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Manuela Milden
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Malte Eck
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Tobias Meckel
- Department of Chemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
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17
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Ayaz G, Turan G, Olgun ÇE, Kars G, Karakaya B, Yavuz K, Demiralay ÖD, Can T, Muyan M, Yaşar P. A prelude to the proximity interaction mapping of CXXC5. Sci Rep 2021; 11:17587. [PMID: 34475492 PMCID: PMC8413330 DOI: 10.1038/s41598-021-97060-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/17/2021] [Indexed: 11/09/2022] Open
Abstract
CXXC5 is a member of the zinc-finger CXXC family proteins that interact with unmodified CpG dinucleotides through a conserved ZF-CXXC domain. CXXC5 is involved in the modulation of gene expressions that lead to alterations in diverse cellular events. However, the underlying mechanism of CXXC5-modulated gene expressions remains unclear. Proteins perform their functions in a network of proteins whose identities and amounts change spatiotemporally in response to various stimuli in a lineage-specific manner. Since CXXC5 lacks an intrinsic transcription regulatory function or enzymatic activity but is a DNA binder, CXXC5 by interacting with proteins could act as a scaffold to establish a chromatin state restrictive or permissive for transcription. To initially address this, we utilized the proximity-dependent biotinylation approach. Proximity interaction partners of CXXC5 include DNA and chromatin modifiers, transcription factors/co-regulators, and RNA processors. Of these, CXXC5 through its CXXC domain interacted with EMD, MAZ, and MeCP2. Furthermore, an interplay between CXXC5 and MeCP2 was critical for a subset of CXXC5 target gene expressions. It appears that CXXC5 may act as a nucleation factor in modulating gene expressions. Providing a prelude for CXXC5 actions, our results could also contribute to a better understanding of CXXC5-mediated cellular processes in physiology and pathophysiology.
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Affiliation(s)
- Gamze Ayaz
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey. .,Cancer and Stem Cell Epigenetics Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Gizem Turan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Çağla Ece Olgun
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Gizem Kars
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Burcu Karakaya
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Kerim Yavuz
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Öykü Deniz Demiralay
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Tolga Can
- Department of Computer Engineering Middle, East Technical University, 06800, Ankara, Turkey
| | - Mesut Muyan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey. .,Cansyl Laboratories, Middle East Technical University, 06800, Ankara, Turkey.
| | - Pelin Yaşar
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey.,Epigenetics and Stem Cell Biology Laboratory, Single Cell Dynamics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
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18
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Sharifi O, Yasui DH. The Molecular Functions of MeCP2 in Rett Syndrome Pathology. Front Genet 2021; 12:624290. [PMID: 33968128 PMCID: PMC8102816 DOI: 10.3389/fgene.2021.624290] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
MeCP2 protein, encoded by the MECP2 gene, binds to DNA and affects transcription. Outside of this activity the true range of MeCP2 function is still not entirely clear. As MECP2 gene mutations cause the neurodevelopmental disorder Rett syndrome in 1 in 10,000 female births, much of what is known about the biologic function of MeCP2 comes from studying human cell culture models and rodent models with Mecp2 gene mutations. In this review, the full scope of MeCP2 research available in the NIH Pubmed (https://pubmed.ncbi.nlm.nih.gov/) data base to date is considered. While not all original research can be mentioned due to space limitations, the main aspects of MeCP2 and Rett syndrome research are discussed while highlighting the work of individual researchers and research groups. First, the primary functions of MeCP2 relevant to Rett syndrome are summarized and explored. Second, the conflicting evidence and controversies surrounding emerging aspects of MeCP2 biology are examined. Next, the most obvious gaps in MeCP2 research studies are noted. Finally, the most recent discoveries in MeCP2 and Rett syndrome research are explored with a focus on the potential and pitfalls of novel treatments and therapies.
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Affiliation(s)
- Osman Sharifi
- LaSalle Laboratory, Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA, United States
| | - Dag H Yasui
- LaSalle Laboratory, Department of Medical Microbiology and Immunology, UC Davis School of Medicine, Davis, CA, United States
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19
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Willbanks A, Wood S, Cheng JX. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes (Basel) 2021; 12:genes12050627. [PMID: 33922187 PMCID: PMC8145807 DOI: 10.3390/genes12050627] [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: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.
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20
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D'Mello SR. MECP2 and the Biology of MECP2 Duplication Syndrome. J Neurochem 2021; 159:29-60. [PMID: 33638179 DOI: 10.1111/jnc.15331] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 11/27/2022]
Abstract
MECP2 duplication syndrome (MDS), a rare X-linked genomic disorder affecting predominantly males, is caused by duplication of the chromosomal region containing the methyl CpG binding protein-2 (MECP2) gene, which encodes methyl-CpG-binding protein 2 (MECP2), a multi-functional protein required for proper brain development and maintenance of brain function during adulthood. Disease symptoms include severe motor and cognitive impairment, delayed or absent speech development, autistic features, seizures, ataxia, recurrent respiratory infections and shortened lifespan. The cellular and molecular mechanisms by which a relatively modest increase in MECP2 protein causes such severe disease symptoms are poorly understood and consequently there are no treatments available for this fatal disorder. This review summarizes what is known to date about the structure and complex regulation of MECP2 and its many functions in the developing and adult brain. Additionally, recent experimental findings on the cellular and molecular underpinnings of MDS based on cell culture and mouse models of the disorder are reviewed. The emerging picture from these studies is that MDS is a neurodegenerative disorder in which neurons die in specific parts of the central nervous system, including the cortex, hippocampus, cerebellum and spinal cord. Neuronal death likely results from astrocytic dysfunction, including a breakdown of glutamate homeostatic mechanisms. The role of elevations in the expression of glial acidic fibrillary protein (GFAP) in astrocytes and the microtubule-associated protein, Tau, in neurons to the pathogenesis of MDS is discussed. Lastly, potential therapeutic strategies to potentially treat MDS are discussed.
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21
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Martins-Ferreira R, Leal B, Costa PP, Ballestar E. Microglial innate memory and epigenetic reprogramming in neurological disorders. Prog Neurobiol 2020; 200:101971. [PMID: 33309803 DOI: 10.1016/j.pneurobio.2020.101971] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/30/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023]
Abstract
Microglia are myeloid-derived cells recognized as brain-resident macrophages. They act as the first and main line of immune defense in the central nervous system (CNS). Microglia have high phenotypic plasticity and are essential for regulating healthy brain homeostasis, and their dysregulation underlies the onset and progression of several CNS pathologies through impaired inflammatory responses. Aberrant microglial activation, following an inflammatory insult, is associated with epigenetic dysregulation in various CNS pathologies. Emerging data suggest that certain stimuli to myeloid cells determine enhanced or attenuated responses to subsequent stimuli. These phenomena, generally termed innate immune memory (IIM), are highly dependent on epigenetic reprogramming. Microglial priming has been reported in several neurological diseases and corresponds to a state of increased permissiveness or exacerbated response, promoted by continuous exposure to a chronic pro-inflammatory environment. In this article, we provide extensive evidence of these epigenetic-mediated phenomena under neurological conditions and discuss their contribution to pathogenesis and their clinical implications, including those concerning potential novel therapeutic approaches.
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Affiliation(s)
- Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain; Immunogenetics Lab, Unit for Multidisciplinary Research in Biomedicine (UMIB), Instituto De Ciências Biomédicas Abel Salazar - Universidade Do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Barbara Leal
- Immunogenetics Lab, Unit for Multidisciplinary Research in Biomedicine (UMIB), Instituto De Ciências Biomédicas Abel Salazar - Universidade Do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Paulo Pinho Costa
- Immunogenetics Lab, Unit for Multidisciplinary Research in Biomedicine (UMIB), Instituto De Ciências Biomédicas Abel Salazar - Universidade Do Porto (ICBAS-UPorto), Rua Jorge Viterbo Ferreira, 228, 4050-313, Porto, Portugal
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain.
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22
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Fernández-Barrena MG, Arechederra M, Colyn L, Berasain C, Avila MA. Epigenetics in hepatocellular carcinoma development and therapy: The tip of the iceberg. JHEP Rep 2020; 2:100167. [PMID: 33134907 PMCID: PMC7585149 DOI: 10.1016/j.jhepr.2020.100167] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a deadly tumour whose causative agents are generally well known, but whose pathogenesis remains poorly understood. Nevertheless, key genetic alterations are emerging from a heterogeneous molecular landscape, providing information on the tumorigenic process from initiation to progression. Among these molecular alterations, those that affect epigenetic processes are increasingly recognised as contributing to carcinogenesis from preneoplastic stages. The epigenetic machinery regulates gene expression through intertwined and partially characterised circuits involving chromatin remodelers, covalent DNA and histone modifications, and dedicated proteins reading these modifications. In this review, we summarise recent findings on HCC epigenetics, focusing mainly on changes in DNA and histone modifications and their carcinogenic implications. We also discuss the potential drugs that target epigenetic mechanisms for HCC treatment, either alone or in combination with current therapies, including immunotherapies.
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Key Words
- 5acC, 5-acetylcytosine
- 5fC, 5-formylcytosine
- 5hmC, 5-hydoxymethyl cytosine
- 5mC, 5-methylcytosine
- Acetyl-CoA, acetyl coenzyme A
- BER, base excision repair
- BRD, bromodomain
- CDA, cytidine deaminase
- CGI, CpG island
- CIMP, CGI methylator phenotype
- CTLA-4, cytotoxic T-lymphocyte-associated protein 4
- DNMT, DNA methyltransferase
- DNMTi, DNMT inhibitor
- Epigenetics
- FAD, flavin adenine dinucleotide
- HAT, histone acetyltransferases
- HCC, hepatocellular carcinoma
- HDAC, histone deacetylase
- HDACi, HDAC inhibitor
- HDM, histone demethylase
- HMT, histone methyltransferase
- Hepatocellular carcinoma
- KMT, lysine methyltransferase
- LSD/KDM, lysine specific demethylases
- NAFLD, non-alcoholic fatty liver disease
- NK, natural killer
- NPC, nasopharyngeal carcinoma
- PD-L1, programmed cell death ligand-1
- PD1, programmed cell death protein 1
- PHD, plant homeodomain
- PTM, post-translational modification
- SAM, S-adenosyl-L-methionine
- TDG, thymidine-DNA-glycosylase
- TERT, telomerase reverse transcriptase
- TET, ten-eleven translocation
- TME, tumour microenvironment
- TSG, tumour suppressor gene
- Therapy
- UHRF1, ubiquitin like with PHD and ring finger domains 1
- VEGF, vascular endothelial growth factor
- ncRNAs, non-coding RNAs
- α-KG, α-ketoglutarate
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Affiliation(s)
- Maite G. Fernández-Barrena
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - María Arechederra
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Leticia Colyn
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
| | - Carmen Berasain
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
| | - Matias A. Avila
- Hepatology Program CIMA, University of Navarra, Pamplona, Spain
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid, Spain
- IdiSNA, Navarra Institute for Health Research, Pamplona, Spain
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23
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Xing H, Cui N, Johnson CM, Faisthalab Z, Jiang C. Dual synaptic inhibitions of brainstem neurons by GABA and glycine with impact on Rett syndrome. J Cell Physiol 2020; 236:3615-3628. [PMID: 33169374 DOI: 10.1002/jcp.30098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/20/2020] [Accepted: 09/24/2020] [Indexed: 12/29/2022]
Abstract
Rett syndrome (RTT) is a neurodevelopmental disease caused mostly by mutations in the MECP2 gene. People with RTT show breathing dysfunction attributable to the high rate of sudden death. Previous studies have shown that insufficient GABA synaptic inhibition contributes to the breathing abnormalities in mouse models of RTT, while it remains elusive how the glycine system is affected. We found that optogenetic stimulation of GAD-expressing neurons in mice produced GABAergic and glycinergic postsynaptic inhibitions of neurons in the hypoglossal nucleus (XII) and the dorsal motor nucleus of vagus (DMNV). By sequential applications of bicuculline and strychnine, such inhibition appeared approximately 44% GABAA ergic and 52% glycinergic in XII neurons, and approximately 49% GABAA ergic and 46% glycinergic in DMNV neurons. Miniature inhibitory postsynaptic potentials (mIPSCs) in these neurons were approximately 47% GABAA ergic and 49% glycinergic in XII neurons, and approximately 48% versus 50% in DMNV neurons, respectively. Consistent with the data, our single-cell polymerase chain reaction studies indicated that transcripts of GABAA receptor γ2 subunit (GABAA Rγ2) and glycine receptor β subunit (GlyRβ) were simultaneously expressed in these cells. In MeCP2R168X mice, proportions of GABAA ergic and glycinergic mIPSCs became approximately 28% versus 69% in XII neurons, and approximately 31% versus 66% in DMNV cells. In comparison with control mice, the GABAA ergic and glycinergic mIPSCs decreased significantly in the XII and DMNV neurons from the MeCP2R168X mice, so did the transcripts of GABAA Rγ2 and GlyRβ. These results suggest that XII and DMNV neurons adopt dual GABAA ergic and glycinergic synaptic inhibitions, and with Mecp2 disruption these neurons rely more on glycinergic synaptic inhibition.
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Affiliation(s)
- Hao Xing
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Ningren Cui
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | | | - Zaakir Faisthalab
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Chun Jiang
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
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24
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Malousi A, Andreou AZ, Kouidou S. In silico structural analysis of sequences containing 5-hydroxymethylcytosine reveals its potential as binding regulator for development, ageing and cancer-related transcription factors. Epigenetics 2020; 16:503-518. [PMID: 32752914 DOI: 10.1080/15592294.2020.1805693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The presence of 5-hydroxymethyl cytosine in DNA has been previously associated with ageing. Using in silico analysis of normal liver samples we presently observed that in 5-hydroxymethyl cytosine sequences, DNA methylation is dependent on the co-presence of G-quadruplexes and palindromes. This association exhibits discrete patterns depending on G-quadruplex and palindrome densities. DNase-Seq data show that 5-hydroxymethyl cytosine sequences are common among liver nucleosomes (p < 2.2x10-16) and threefold more frequent than nucleosome sequences. Nucleosomes lacking palindromes and potential G-quadruplexes are rare in vivo (1%) and nucleosome occupancy potential decreases with increasing G-quadruplexes. Palindrome distribution is similar to that previously reported in nucleosomes. In low and mixed complexity sequences 5-hydroxymethyl cytosine is frequently located next to three elements: G-quadruplexes or imperfect G-quadruplexes with CpGs, or unstable hairpin loops (TCCCAY6TGGGA) mostly located in antisense strands or finally A-/T-rich segments near these motifs. The high frequencies and selective distribution of pentamer sequences (including TCCCA, TGGGA) probably indicate the positive contribution of 5-hydroxymethyl cytosine to stabilize the formation of structures unstable in the absence of this cytosine modification. Common motifs identified in all total 5-hydroxymethyl cytosine-containing sequences exhibit high homology to recognition sites of several transcription factor families: homeobox, factors involved in growth, mortality/ageing, cancer, neuronal function, vision, and reproduction. We conclude that cytosine hydroxymethylation could play a role in the recognition of sequences with G-quadruplexes/palindromes by forming epigenetically regulated DNA 'springs' and governing expansions or compressions recognized by different transcription factors or stabilizing nucleosomes. The balance of these epigenetic elements is lost in hepatocellular carcinoma.
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Affiliation(s)
- Andigoni Malousi
- Lab. of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Sofia Kouidou
- Lab. of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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