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Yang F, Guo X, Bao Y, Li R. The role of ribosomal DNA methylation in embryonic development, aging and diseases. Epigenetics Chromatin 2024; 17:23. [PMID: 39085958 PMCID: PMC11290161 DOI: 10.1186/s13072-024-00548-4] [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: 05/27/2024] [Accepted: 07/11/2024] [Indexed: 08/02/2024] Open
Abstract
The ribosomal DNA (rDNA) constitutes a remarkably conserved DNA sequence within species, located in the area of the nucleolus, and responsible for coding three major types of rRNAs (18S, 5.8S and 28S). While historical investigations into rDNA focused on its structure and coding capabilities, recent research has turned to explore its functional roles in various biological processes. In this review, we summarize the main findings of rDNA methylation with embryonic development, aging and diseases in multiple species, including epigenetic alterations, related biological processes and potential applications of rDNA methylation. We present an overview of current related research and identify gaps in this field.
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Affiliation(s)
- Fei Yang
- National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xutong Guo
- National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiming Bao
- National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Rujiao Li
- National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
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Yang C, Liu G, Chen X, Le W. Cerebellum in Alzheimer's disease and other neurodegenerative diseases: an emerging research frontier. MedComm (Beijing) 2024; 5:e638. [PMID: 39006764 PMCID: PMC11245631 DOI: 10.1002/mco2.638] [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: 10/30/2023] [Revised: 06/04/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024] Open
Abstract
The cerebellum is crucial for both motor and nonmotor functions. Alzheimer's disease (AD), alongside other dementias such as vascular dementia (VaD), Lewy body dementia (DLB), and frontotemporal dementia (FTD), as well as other neurodegenerative diseases (NDs) like Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), and spinocerebellar ataxias (SCA), are characterized by specific and non-specific neurodegenerations in central nervous system. Previously, the cerebellum's significance in these conditions was underestimated. However, advancing research has elevated its profile as a critical node in disease pathology. We comprehensively review the existing evidence to elucidate the relationship between cerebellum and the aforementioned diseases. Our findings reveal a growing body of research unequivocally establishing a link between the cerebellum and AD, other forms of dementia, and other NDs, supported by clinical evidence, pathological and biochemical profiles, structural and functional neuroimaging data, and electrophysiological findings. By contrasting cerebellar observations with those from the cerebral cortex and hippocampus, we highlight the cerebellum's distinct role in the disease processes. Furthermore, we also explore the emerging therapeutic potential of targeting cerebellum for the treatment of these diseases. This review underscores the importance of the cerebellum in these diseases, offering new insights into the disease mechanisms and novel therapeutic strategies.
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Affiliation(s)
- Cui Yang
- Institute of Neurology Sichuan Provincial People's Hospital School of Medicine University of Electronic Science and Technology of China Chengdu China
| | - Guangdong Liu
- Institute of Neurology Sichuan Provincial People's Hospital School of Medicine University of Electronic Science and Technology of China Chengdu China
| | - Xi Chen
- Institute of Neurology Sichuan Provincial People's Hospital School of Medicine University of Electronic Science and Technology of China Chengdu China
| | - Weidong Le
- Institute of Neurology Sichuan Provincial People's Hospital School of Medicine University of Electronic Science and Technology of China Chengdu China
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Ravaioli F, Bacalini MG, Giuliani C, Pellegrini C, D’Silva C, De Fanti S, Pirazzini C, Giorgi G, Del Re B. Evaluation of DNA Methylation Profiles of LINE-1, Alu and Ribosomal DNA Repeats in Human Cell Lines Exposed to Radiofrequency Radiation. Int J Mol Sci 2023; 24:9380. [PMID: 37298336 PMCID: PMC10253908 DOI: 10.3390/ijms24119380] [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: 04/24/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
A large body of evidence indicates that environmental agents can induce alterations in DNA methylation (DNAm) profiles. Radiofrequency electromagnetic fields (RF-EMFs) are radiations emitted by everyday devices, which have been classified as "possibly carcinogenic"; however, their biological effects are unclear. As aberrant DNAm of genomic repetitive elements (REs) may promote genomic instability, here, we sought to determine whether exposure to RF-EMFs could affect DNAm of different classes of REs, such as long interspersed nuclear elements-1 (LINE-1), Alu short interspersed nuclear elements and ribosomal repeats. To this purpose, we analysed DNAm profiles of cervical cancer and neuroblastoma cell lines (HeLa, BE(2)C and SH-SY5Y) exposed to 900 MHz GSM-modulated RF-EMF through an Illumina-based targeted deep bisulfite sequencing approach. Our findings showed that radiofrequency exposure did not affect the DNAm of Alu elements in any of the cell lines analysed. Conversely, it influenced DNAm of LINE-1 and ribosomal repeats in terms of both average profiles and organisation of methylated and unmethylated CpG sites, in different ways in each of the three cell lines studied.
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Affiliation(s)
- Francesco Ravaioli
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, 40126 Bologna, Italy;
| | - Camilla Pellegrini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Chiara D’Silva
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Sara De Fanti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Chiara Pirazzini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Gianfranco Giorgi
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
| | - Brunella Del Re
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
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Ravaioli F, Zampieri M, Morandi L, Pirazzini C, Pellegrini C, De Fanti S, Gensous N, Pirazzoli GL, Sambati L, Ghezzo A, Ciccarone F, Reale A, Monti D, Salvioli S, Caiafa P, Capri M, Bürkle A, Moreno-Villanueva M, Garagnani P, Franceschi C, Bacalini MG. DNA Methylation Analysis of Ribosomal DNA in Adults With Down Syndrome. Front Genet 2022; 13:792165. [PMID: 35571061 PMCID: PMC9094685 DOI: 10.3389/fgene.2022.792165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 03/18/2022] [Indexed: 01/08/2023] Open
Abstract
Control of ribosome biogenesis is a critical aspect of the regulation of cell metabolism. As ribosomal genes (rDNA) are organized in repeated clusters on chromosomes 13, 14, 15, 21, and 22, trisomy of chromosome 21 confers an excess of rDNA copies to persons with Down syndrome (DS). Previous studies showed an alteration of ribosome biogenesis in children with DS, but the epigenetic regulation of rDNA genes has not been investigated in adults with DS so far. In this study, we used a targeted deep-sequencing approach to measure DNA methylation (DNAm) of rDNA units in whole blood from 69 adults with DS and 95 euploid controls. We further evaluated the expression of the precursor of ribosomal RNAs (RNA45S) in peripheral blood mononuclear cells (PBMCs) from the same subjects. We found that the rDNA promoter tends to be hypermethylated in DS concerning the control group. The analysis of epihaplotypes (the combination of methylated and unmethylated CpG sites along the same DNA molecule) showed a significantly lower intra-individual diversity in the DS group, which at the same time was characterized by a higher interindividual variability. Finally, we showed that RNA45S expression is lower in adults with DS. Collectively, our results suggest a rearrangement of the epigenetic profile of rDNA in DS, possibly to compensate for the extranumerary rDNA copies. Future studies should assess whether the regulation of ribosome biogenesis can contribute to the pathogenesis of DS and explain the clinical heterogeneity characteristic of the syndrome.
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Affiliation(s)
- Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Luca Morandi
- Functional and Molecular Neuroimaging Unit, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Noémie Gensous
- Department of Internal Medicine and Clinical Immunology, CHU Bordeaux (Groupe Hospitalier Saint-André), Bordeaux, France
- UMR/CNRS 5164, ImmunoConcEpT, CNRS, University of Bordeaux, Bordeaux, France
| | | | - Luisa Sambati
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, U.O.C. Clinica Neurologica Rete Neurologica Metropolitana (NEUROMET), Bologna, Italy
| | | | - Fabio Ciccarone
- IRCCS San Raffaele Roma, Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy
| | - Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Rome, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Maria Moreno-Villanueva
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”—Unit of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
- *Correspondence: Maria Giulia Bacalini,
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