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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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2
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Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Pericentromeric satellite RNAs as flexible protein partners in the regulation of nuclear structure. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1868. [PMID: 38973000 DOI: 10.1002/wrna.1868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024]
Abstract
Pericentromeric heterochromatin is mainly composed of satellite DNA sequences. Although being historically associated with transcriptional repression, some pericentromeric satellite DNA sequences are transcribed. The transcription events of pericentromeric satellite sequences occur in highly flexible biological contexts. Hence, the apparent randomness of pericentromeric satellite transcription incites the discussion about the attribution of biological functions. However, pericentromeric satellite RNAs have clear roles in the organization of nuclear structure. Silencing pericentromeric heterochromatin depends on pericentromeric satellite RNAs, that, in a feedback mechanism, contribute to the repression of pericentromeric heterochromatin. Moreover, pericentromeric satellite RNAs can also act as scaffolding molecules in condensate subnuclear structures (e.g., nuclear stress bodies). Since the formation/dissociation of nuclear condensates provides cell adaptability, pericentromeric satellite RNAs can be an epigenetic platform for regulating (sub)nuclear structure. We review current knowledge about pericentromeric satellite RNAs that, irrespective of the meaning of biological function, should be functionally addressed in regular and disease settings. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Mariana Lopes
- CytoGenomics Lab-Department of Genetics and Biotechnology (DGB), University of Trás os Montes and Alto Douro (UTAD), Vila Real, Portugal
- BioISI: Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Sandra Louzada
- CytoGenomics Lab-Department of Genetics and Biotechnology (DGB), University of Trás os Montes and Alto Douro (UTAD), Vila Real, Portugal
- BioISI: Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- BioISI: Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
| | - Raquel Chaves
- CytoGenomics Lab-Department of Genetics and Biotechnology (DGB), University of Trás os Montes and Alto Douro (UTAD), Vila Real, Portugal
- BioISI: Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisbon, Portugal
- RISE-Health: Health Research Network, Faculty of Medicine, University of Porto, Porto, Portugal
- CACTMAD: Trás-os-Montes and Alto Douro Academic Clinic Center,University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
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3
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Choi J, Kim T, Cho EJ. HIRA vs. DAXX: the two axes shaping the histone H3.3 landscape. Exp Mol Med 2024; 56:251-263. [PMID: 38297159 PMCID: PMC10907377 DOI: 10.1038/s12276-023-01145-3] [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: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 02/02/2024] Open
Abstract
H3.3, the most common replacement variant for histone H3, has emerged as an important player in chromatin dynamics for controlling gene expression and genome integrity. While replicative variants H3.1 and H3.2 are primarily incorporated into nucleosomes during DNA synthesis, H3.3 is under the control of H3.3-specific histone chaperones for spatiotemporal incorporation throughout the cell cycle. Over the years, there has been progress in understanding the mechanisms by which H3.3 affects domain structure and function. Furthermore, H3.3 distribution and relative abundance profoundly impact cellular identity and plasticity during normal development and pathogenesis. Recurrent mutations in H3.3 and its chaperones have been identified in neoplastic transformation and developmental disorders, providing new insights into chromatin biology and disease. Here, we review recent findings emphasizing how two distinct histone chaperones, HIRA and DAXX, take part in the spatial and temporal distribution of H3.3 in different chromatin domains and ultimately achieve dynamic control of chromatin organization and function. Elucidating the H3.3 deposition pathways from the available histone pool will open new avenues for understanding the mechanisms by which H3.3 epigenetically regulates gene expression and its impact on cellular integrity and pathogenesis.
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Affiliation(s)
- Jinmi Choi
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Taewan Kim
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Eun-Jung Cho
- Sungkyunkwan University School of Pharmacy, Seoburo 2066, Jangan-gu Suwon, Gyeonggi-do, 16419, Republic of Korea.
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4
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Yin Y, Shen X. Noncoding RNA-chromatin association: Functions and mechanisms. FUNDAMENTAL RESEARCH 2023; 3:665-675. [PMID: 38933302 PMCID: PMC11197541 DOI: 10.1016/j.fmre.2023.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/12/2023] [Accepted: 03/23/2023] [Indexed: 06/28/2024] Open
Abstract
Pervasive transcription of the mammalian genome produces hundreds of thousands of noncoding RNAs (ncRNAs). Numerous studies have suggested that some of these ncRNAs regulate multiple cellular processes and play important roles in physiological and pathological processes. Notably, a large subset of ncRNAs is enriched on chromatin and participates in regulating gene expression and the dynamics of chromatin structure and status. In this review, we summarize recent advances in the functional study of chromatin-associated ncRNAs and mechanistic insights into how these ncRNAs associate with chromatin. We also discuss the potential future challenges which still need to be overcome in this field.
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Affiliation(s)
- Yafei Yin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Yuhangtang Road, Hangzhou, Zhejiang 310058, China
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China
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5
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Agredo A, Kasinski AL. Histone 4 lysine 20 tri-methylation: a key epigenetic regulator in chromatin structure and disease. Front Genet 2023; 14:1243395. [PMID: 37671044 PMCID: PMC10475950 DOI: 10.3389/fgene.2023.1243395] [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: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 09/07/2023] Open
Abstract
Chromatin is a vital and dynamic structure that is carefully regulated to maintain proper cell homeostasis. A great deal of this regulation is dependent on histone proteins which have the ability to be dynamically modified on their tails via various post-translational modifications (PTMs). While multiple histone PTMs are studied and often work in concert to facilitate gene expression, here we focus on the tri-methylation of histone H4 on lysine 20 (H4K20me3) and its function in chromatin structure, cell cycle, DNA repair, and development. The recent studies evaluated in this review have shed light on how H4K20me3 is established and regulated by various interacting partners and how H4K20me3 and the proteins that interact with this PTM are involved in various diseases. Through analyzing the current literature on H4K20me3 function and regulation, we aim to summarize this knowledge and highlights gaps that remain in the field.
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Affiliation(s)
- Alejandra Agredo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Life Sciences Interdisciplinary Program (PULSe), Purdue University, West Lafayette, IN, United States
| | - Andrea L. Kasinski
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
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6
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Schirone L, Vecchio D, Valenti V, Forte M, Relucenti M, Angelini A, Zaglia T, Schiavon S, D'Ambrosio L, Sarto G, Stanzione R, Mangione E, Miglietta S, Di Bona A, Fedrigo M, Ghigo A, Versaci F, Petrozza V, Marchitti S, Rubattu S, Volpe M, Sadoshima J, Frati L, Frati G, Sciarretta S. MST1 mediates doxorubicin-induced cardiomyopathy by SIRT3 downregulation. Cell Mol Life Sci 2023; 80:245. [PMID: 37566283 PMCID: PMC10421787 DOI: 10.1007/s00018-023-04877-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/30/2023] [Accepted: 07/16/2023] [Indexed: 08/12/2023]
Abstract
Heart failure is a major side effect of doxorubicin (DOX) treatment in patients with cancer. However, the mechanisms underlying the development of DOX-induced heart failure need to be addressed. This study aims to test whether the serine/threonine kinase MST1, a major Hippo pathway component, contributes to the development of DOX-induced myocardial injury. C57BL/6J WT mice and mice with cardiomyocyte-specific dominant-negative MST1 (kinase-dead) overexpression received three weekly injections of DOX, reaching a final cumulative dose of 18 mg/kg. Echocardiographic, histological and biochemical analyses were performed six weeks after the first DOX administration. The effects of MST1 inhibition on DOX-induced cardiomyocyte injury were also tested in vitro. MST1 signaling was significantly activated in cardiomyocytes in response to DOX treatment in vitro and in vivo. Wild-type (WT) mice treated with DOX developed cardiac dysfunction and mitochondrial abnormalities. However, these detrimental effects were abolished in mice with cardiomyocyte-specific overexpression of dominant-negative MST1 (DN-MST1) or treated with XMU-MP-1, a specific MST1 inhibitor, indicating that MST1 inhibition attenuates DOX-induced cardiac dysfunction. DOX treatment led to a significant downregulation of cardiac levels of SIRT3, a deacetylase involved in mitochondrial protection, in WT mice, which was rescued by MST1 inhibition. Pharmacological inhibition of SIRT3 blunted the protective effects of MST1 inhibition, indicating that SIRT3 downregulation mediates the cytotoxic effects of MST1 activation in response to DOX treatment. Finally, we found a significant upregulation of MST1 and downregulation of SIRT3 levels in human myocardial tissue of cancer patients treated with DOX. In summary, MST1 contributes to DOX-induced cardiomyopathy through SIRT3 downregulation.
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Affiliation(s)
- Leonardo Schirone
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Daniele Vecchio
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Valentina Valenti
- Department of Cardiology, Santa Maria Goretti Hospital, Latina, Italy
| | | | - Michela Relucenti
- Department of Anatomical, Sapienza University of Rome, Histological, Forensic Medicine and Orthopaedic Sciences, Rome, Italy
| | - Annalisa Angelini
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padova Medical School, Padua, Italy
| | - Tania Zaglia
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padova Medical School, Padua, Italy
- Veneto Institute of Molecular Medicine, Padua, Italy
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Sonia Schiavon
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Luca D'Ambrosio
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Gianmarco Sarto
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | | | | | - Selenia Miglietta
- Department of Anatomical, Sapienza University of Rome, Histological, Forensic Medicine and Orthopaedic Sciences, Rome, Italy
| | - Anna Di Bona
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padova Medical School, Padua, Italy
| | - Marny Fedrigo
- Department of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padova Medical School, Padua, Italy
| | - Alessandra Ghigo
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Turin, Italy
| | - Francesco Versaci
- Department of Cardiology, Santa Maria Goretti Hospital, Latina, Italy
| | - Vincenzo Petrozza
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | | | - Speranza Rubattu
- IRCCS Neuromed, Pozzilli, Italy
- Department of Clinical and Molecular Medicine, (Sapienza University of Rome, S. Andrea Hospital), Rome, Italy
| | - Massimo Volpe
- Department of Clinical and Molecular Medicine, (Sapienza University of Rome, S. Andrea Hospital), Rome, Italy
- IRCCS San Raffaele, Rome, Italy
| | - Junichi Sadoshima
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Cardiovascular Research Institute, Newark, NJ, USA
| | - Luigi Frati
- IRCCS Neuromed, Pozzilli, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
| | - Giacomo Frati
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
- IRCCS Neuromed, Pozzilli, Italy
| | - Sebastiano Sciarretta
- Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.
- IRCCS Neuromed, Pozzilli, Italy.
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7
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Forte M, Marchitti S, Di Nonno F, Stanzione R, Schirone L, Cotugno M, Bianchi F, Schiavon S, Raffa S, Ranieri D, Fioriniello S, Della Ragione F, Torrisi MR, Carnevale R, Valenti V, Versaci F, Frati G, Vecchione C, Volpe M, Rubattu S, Sciarretta S. NPPA/atrial natriuretic peptide is an extracellular modulator of autophagy in the heart. Autophagy 2023; 19:1087-1099. [PMID: 35998113 PMCID: PMC10012953 DOI: 10.1080/15548627.2022.2115675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 12/09/2022] Open
Abstract
NPPA/atrial natriuretic peptide (natriuretic peptide type A) exerts critical pleiotropic effects in the cardiovascular system, limiting cardiomyocyte hypertrophy and death, reducing cardiac fibrosis and promoting vascular integrity. However, the molecular mechanisms underlying these beneficial effects still need to be clarified. We demonstrated for the first time that macroautophagy/autophagy is involved in the local protective effects of NPPA in cardiomyocytes (CMs), both in vitro and in vivo. Exogenous NPPA rapidly activates autophagy in CMs through NPR1/type A natriuretic peptide receptor and PRKG/protein kinase G signaling and also increases cardiac autophagy in mice. Remarkably, endogenous NPPA is secreted by CMs in response to glucose deprivation or hypoxia, thereby stimulating autophagy through autocrine/paracrine mechanisms. NPPA preserves cell viability and reduces hypertrophy in response to stress through autophagy activation. In vivo, we found that Nppa knockout mice undergoing ischemia-reperfusion (I/R) show increased infarct size and reduced autophagy. Reactivation of autophagy by Tat-Beclin D11 limits I/R injury. We also found that the protective effects of NPPA in reducing infarct size are abrogated in the presence of autophagy inhibition. Mechanistically, we found that NPPA stimulates autophagy through the activation of TFEB (transcription factor EB). Our data suggest that NPPA is a novel extracellular regulator of autophagy in the heart.
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Affiliation(s)
- Maurizio Forte
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
| | - Simona Marchitti
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
| | - Flavio Di Nonno
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
| | - Rosita Stanzione
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
| | - Leonardo Schirone
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
- Department of Internal, Anesthetic and Cardiovascular Clinical Sciences, “La Sapienza” University of Rome, Rome, Italy
| | - Maria Cotugno
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
| | - Franca Bianchi
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
| | - Sonia Schiavon
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Salvatore Raffa
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Rome
| | - Danilo Ranieri
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Rome
| | - Salvatore Fioriniello
- Institute of Genetics and Biophysics (IGB), Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Floriana Della Ragione
- Institute of Genetics and Biophysics (IGB), Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Maria Rosaria Torrisi
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Rome
| | - Roberto Carnevale
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
- Mediterranea Cardiocentro, via Orazio, Naples, Italy
| | - Valentina Valenti
- Department of Cardiology, Ospedale Santa Maria Goretti, Latina, Italy
| | - Francesco Versaci
- Department of Cardiology, Ospedale Santa Maria Goretti, Latina, Italy
| | - Giacomo Frati
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Carmine Vecchione
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
- Department of Medicine, Surgery and Dentistry, “Scuola Medica Salernitana”, University of Salerno, Baronissi (SA), Italy
| | - Massimo Volpe
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Rome
| | - Speranza Rubattu
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
- Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Rome
| | - Sebastiano Sciarretta
- Department of Angio Cardio Neurology, IRCCS Neuromed, Pozzilli, Italy
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
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8
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Pepe G, Fioriniello S, Marracino F, Capocci L, Maglione V, D'Esposito M, Di Pardo A, Della Ragione F. Blood–Brain Barrier Integrity Is Perturbed in a Mecp2-Null Mouse Model of Rett Syndrome. Biomolecules 2023; 13:biom13040606. [PMID: 37189354 DOI: 10.3390/biom13040606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Rett syndrome (RTT, online MIM 312750) is a devastating neurodevelopmental disorder characterized by motor and cognitive disabilities. It is mainly caused by pathogenetic variants in the X-linked MECP2 gene, encoding an epigenetic factor crucial for brain functioning. Despite intensive studies, the RTT pathogenetic mechanism remains to be fully elucidated. Impaired vascular function has been previously reported in RTT mouse models; however, whether an altered brain vascular homeostasis and the subsequent blood–brain barrier (BBB) breakdown occur in RTT and contribute to the disease-related cognitive impairment is still unknown. Interestingly, in symptomatic Mecp2-null (Mecp2-/y, Mecp2tm1.1Bird) mice, we found enhanced BBB permeability associated with an aberrant expression of the tight junction proteins Ocln and Cldn-5 in different brain areas, in terms of both transcript and protein levels. Additionally, Mecp2-null mice showed an altered expression of different genes encoding factors with a role in the BBB structure and function, such as Cldn3, Cldn12, Mpdz, Jam2, and Aqp4. With this study, we provide the first evidence of impaired BBB integrity in RTT and highlight a potential new molecular hallmark of the disease that might open new perspectives for the setting-up of novel therapeutic strategies.
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Affiliation(s)
| | - Salvatore Fioriniello
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
| | | | | | | | - Maurizio D'Esposito
- IRCCS Neuromed, 86077 Pozzilli, Italy
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
| | | | - Floriana Della Ragione
- IRCCS Neuromed, 86077 Pozzilli, Italy
- Institute of Genetics and Biophysics 'A. Buzzati-Traverso', CNR, 80131 Naples, Italy
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9
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Novo CL, Wong EV, Hockings C, Poudel C, Sheekey E, Wiese M, Okkenhaug H, Boulton SJ, Basu S, Walker S, Kaminski Schierle GS, Narlikar GJ, Rugg-Gunn PJ. Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells. Nat Commun 2022; 13:3525. [PMID: 35725842 PMCID: PMC9209518 DOI: 10.1038/s41467-022-31198-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/07/2022] [Indexed: 12/25/2022] Open
Abstract
Heterochromatin maintains genome integrity and function, and is organised into distinct nuclear domains. Some of these domains are proposed to form by phase separation through the accumulation of HP1ɑ. Mouse heterochromatin contains noncoding major satellite repeats (MSR), which are highly transcribed in mouse embryonic stem cells (ESCs). Here, we report that MSR transcripts can drive the formation of HP1ɑ droplets in vitro, and modulate heterochromatin into dynamic condensates in ESCs, contributing to the formation of large nuclear domains that are characteristic of pluripotent cells. Depleting MSR transcripts causes heterochromatin to transition into a more compact and static state. Unexpectedly, changing heterochromatin's biophysical properties has severe consequences for ESCs, including chromosome instability and mitotic defects. These findings uncover an essential role for MSR transcripts in modulating the organisation and properties of heterochromatin to preserve genome stability. They also provide insights into the processes that could regulate phase separation and the functional consequences of disrupting the properties of heterochromatin condensates.
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Affiliation(s)
- Clara Lopes Novo
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
- Tommy's National Miscarriage Research Centre at Imperial College London, London, W12 0NN, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Emily V Wong
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Colin Hockings
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Chetan Poudel
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS, UK
| | - Eleanor Sheekey
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Meike Wiese
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Hanneke Okkenhaug
- Imaging Facility, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Artios Pharma Ltd., B940, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Srinjan Basu
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Simon Walker
- Imaging Facility, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | | | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Peter J Rugg-Gunn
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
- Wellcome - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
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10
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Transcriptomic and Epigenomic Landscape in Rett Syndrome. Biomolecules 2021; 11:biom11070967. [PMID: 34209228 PMCID: PMC8301932 DOI: 10.3390/biom11070967] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022] Open
Abstract
Rett syndrome (RTT) is an extremely invalidating, cureless, developmental disorder, and it is considered one of the leading causes of intellectual disability in female individuals. The vast majority of RTT cases are caused by de novo mutations in the X-linked Methyl-CpG binding protein 2 (MECP2) gene, which encodes a multifunctional reader of methylated DNA. MeCP2 is a master epigenetic modulator of gene expression, with a role in the organization of global chromatin architecture. Based on its interaction with multiple molecular partners and the diverse epigenetic scenario, MeCP2 triggers several downstream mechanisms, also influencing the epigenetic context, and thus leading to transcriptional activation or repression. In this frame, it is conceivable that defects in such a multifaceted factor as MeCP2 lead to large-scale alterations of the epigenome, ranging from an unbalanced deposition of epigenetic modifications to a transcriptional alteration of both protein-coding and non-coding genes, with critical consequences on multiple downstream biological processes. In this review, we provide an overview of the current knowledge concerning the transcriptomic and epigenomic alterations found in RTT patients and animal models.
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11
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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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12
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Imaizumi Y, Feil R. Emerging chromatin structural roles of the methyl-CpG binding protein MeCP2. Epigenomics 2021; 13:405-409. [PMID: 33685235 DOI: 10.2217/epi-2021-0053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Yui Imaizumi
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 1919 route de Mende, 34293 Montpellier, France.,University of Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 1919 route de Mende, 34293 Montpellier, France.,University of Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
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13
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Good KV, Vincent JB, Ausió J. MeCP2: The Genetic Driver of Rett Syndrome Epigenetics. Front Genet 2021; 12:620859. [PMID: 33552148 PMCID: PMC7859524 DOI: 10.3389/fgene.2021.620859] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Mutations in methyl CpG binding protein 2 (MeCP2) are the major cause of Rett syndrome (RTT), a rare neurodevelopmental disorder with a notable period of developmental regression following apparently normal initial development. Such MeCP2 alterations often result in changes to DNA binding and chromatin clustering ability, and in the stability of this protein. Among other functions, MeCP2 binds to methylated genomic DNA, which represents an important epigenetic mark with broad physiological implications, including neuronal development. In this review, we will summarize the genetic foundations behind RTT, and the variable degrees of protein stability exhibited by MeCP2 and its mutated versions. Also, past and emerging relationships that MeCP2 has with mRNA splicing, miRNA processing, and other non-coding RNAs (ncRNA) will be explored, and we suggest that these molecules could be missing links in understanding the epigenetic consequences incurred from genetic ablation of this important chromatin modifier. Importantly, although MeCP2 is highly expressed in the brain, where it has been most extensively studied, the role of this protein and its alterations in other tissues cannot be ignored and will also be discussed. Finally, the additional complexity to RTT pathology introduced by structural and functional implications of the two MeCP2 isoforms (MeCP2-E1 and MeCP2-E2) will be described. Epigenetic therapeutics are gaining clinical popularity, yet treatment for Rett syndrome is more complicated than would be anticipated for a purely epigenetic disorder, which should be taken into account in future clinical contexts.
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Affiliation(s)
- Katrina V. Good
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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14
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Feliciello I, Pezer Ž, Sermek A, Bruvo Mađarić B, Ljubić S, Ugarković Đ. Satellite DNA-Mediated Gene Expression Regulation: Physiological and Evolutionary Implication. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:145-167. [PMID: 34386875 DOI: 10.1007/978-3-030-74889-0_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Satellite DNAs are tandemly repeated sequences organized in large clusters within (peri)centromeric and/or subtelomeric heterochromatin. However, in many species, satellite DNAs are not restricted to heterochromatin but are also dispersed as short arrays within euchromatin. Such genomic organization together with transcriptional activity seems to be a prerequisite for the gene-modulatory effect of satellite DNAs which was first demonstrated in the beetle Tribolium castaneum upon heat stress. Namely, enrichment of a silent histone mark at euchromatic repeats of a major beetle satellite DNA results in epigenetic silencing of neighboring genes. In addition, human satellite III transcripts induced by heat shock contribute to genome-wide gene silencing, providing protection against stress-induced cell death. Gene silencing mediated by satellite RNA was also shown to be fundamental for the early embryonic development of the mosquito Aedes aegypti. Apart from a physiological role during embryogenesis and heat stress response, activation of satellite DNAs in terms of transcription and proliferation can have an evolutionary impact. Spreading of satellite repeats throughout euchromatin promotes the variation of epigenetic landscapes and gene expression diversity, contributing to the evolution of gene regulatory networks and to genome adaptation in fluctuating environmental conditions.
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Affiliation(s)
- Isidoro Feliciello
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.,Dipartimento di Medicina Clinica e Chirurgia, Universita' degli Studi di Napoli Federico II, Naples, Italy
| | - Željka Pezer
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antonio Sermek
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Sven Ljubić
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Đurđica Ugarković
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
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15
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Abstract
Here we outline the contents of Stem Cell Reports' first special issue, on chromatin and nuclear architecture in stem cells. It features both reviews and original research articles, covering emerging topics in nuclear architecture including 3D genome organization in stem cells and early development, membraneless organelles, epigenetics-related therapy, and more.
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Affiliation(s)
- Eran Meshorer
- Department of Genetics, The Institute of Life Sciences and The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Israel.
| | - Kathrin Plath
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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