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Golubenko MV, Puzyrev VP. Liberties of the genome: insertions of mitochondrial DNA fragments into nuclear genome. Vavilovskii Zhurnal Genet Selektsii 2024; 28:467-475. [PMID: 39280847 PMCID: PMC11393654 DOI: 10.18699/vjgb-24-53] [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: 02/28/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 09/18/2024] Open
Abstract
The transition of detached fragments of mitochondrial DNA into the nucleus and their integration into chromosomal DNA is a special kind of genetic variability that highlights the relation between the two genomes and their interaction in a eukaryotic cell. The human genome contains several hundreds of insertions of mtDNA fragments (NUMTS). This paper presents an overview of the current state of research in this area. To date, evidence has been obtained that the occurrence of new mtDNA insertions in the nuclear genome is a seldom but not exceptionally rare event. The integration of new mtDNA fragments into the nuclear genome occurs during double-strand DNA break repair through the non-homologous end joining mechanism. Along with evolutionarily stable "genetic fossils" that were integrated into the nuclear genome millions of years ago and are shared by many species, there are NUMTS that could be species-specific, polymorphic in a species, or "private". Partial copies of mitochondrial DNA in the human nuclear genome can interfere with mtDNA during experimental studies of the mitochondrial genome, such as genotyping, heteroplasmy assessment, mtDNA methylation analysis, and mtDNA copy number estimation. In some cases, the insertion of multiple copies of the complete mitochondrial genome sequence may mimic paternal inheritance of mtDNA. The functional significance of NUMTS is poorly understood. For instance, they may be a source of variability for expression and splicing modulation. The role of NUMTS as a cause of hereditary diseases is negligible, since only a few cases of diseases caused by NUMTS have been described so far. In addition, NUMTS can serve as markers for evolutionary genetic studies. Of particular interest is the meaning of NUMTS in eukaryotic genome evolution. The constant flow of functionally inactive DNA sequences from mitochondria into the nucleus and its significance could be studied in view of the modern concepts of evolutionary theory suggesting non-adaptive complexity and the key role of stochastic processes in the formation of genomic structure.
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Affiliation(s)
- M V Golubenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V P Puzyrev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
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Klokkaris A, Migdalska-Richards A. An Overview of Epigenetic Changes in the Parkinson's Disease Brain. Int J Mol Sci 2024; 25:6168. [PMID: 38892355 PMCID: PMC11172855 DOI: 10.3390/ijms25116168] [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: 05/05/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Parkinson's disease is a progressive neurodegenerative disorder, predominantly of the motor system. Although some genetic components and cellular mechanisms of Parkinson's have been identified, much is still unknown. In recent years, emerging evidence has indicated that non-DNA-sequence variation (in particular epigenetic mechanisms) is likely to play a crucial role in the development and progression of the disease. Here, we present an up-to-date overview of epigenetic processes including DNA methylation, DNA hydroxymethylation, histone modifications and non-coding RNAs implicated in the brain of those with Parkinson's disease. We will also discuss the limitations of current epigenetic research in Parkinson's disease, the advantages of simultaneously studying genetics and epigenetics, and putative novel epigenetic therapies.
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Affiliation(s)
| | - Anna Migdalska-Richards
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK;
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Alvarez S, Vanasco V, Adán Areán JS, Magnani N, Evelson P. Mitochondrial Mechanisms in Immunity and Inflammatory Conditions: Beyond Energy Management. Antioxid Redox Signal 2024. [PMID: 38062738 DOI: 10.1089/ars.2023.0367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Significance: The growing importance of mitochondria in the immune response and inflammation is multifaceted. Unraveling the different mechanisms by which mitochondria have a relevant role in the inflammatory response beyond the energy management of the process is necessary for improving our understanding of the host immune defense and the pathogenesis of various inflammatory diseases and syndromes. Critical Issues: Mitochondria are relevant in the immune response at different levels, including releasing activation molecules, changing its structure and function to accompany the immune response, and serving as a structural base for activating intermediates as NLRP3 inflammasome. In this scientific journey of dissecting mitochondrial mechanisms, new questions and interesting aspects arise, such as the involvement of mitochondrial-derived vesicles in the immune response with the putative role of preventing uncontrolled situations. Recent Advances: Researchers are continuously rethinking the role of mitochondria in acute and chronic inflammation and related disorders. As such, mitochondria have important roles as centrally positioned signaling hubs in regulating inflammatory and immune responses. In this review, we present the current understanding of mitochondrial mechanisms involved, beyond the largely known mitochondrial dysfunction, in the onset and development of inflammatory situations. Future Directions: Mitochondria emerge as an interesting and multifaceted platform for studying and developing pharmaceutical and therapeutic approaches. There are many ongoing studies aimed to describe the effects of specific mitochondrial targeted molecules and treatments to ameliorate the consequences of exacerbated inflammatory components of pathologies and syndromes, resulting in an open area of increasing research interest.
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Affiliation(s)
- Silvia Alvarez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Fisicoquímica, CABA, Argentina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
| | - Virginia Vanasco
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Fisicoquímica, CABA, Argentina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
| | - Juan Santiago Adán Areán
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Fisicoquímica, CABA, Argentina
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
| | - Natalia Magnani
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Bioquímica y Medicina Molecular (IBIMOL), Buenos Aires, CABA, Argentina
| | - Pablo Evelson
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Ciencias Químicas, Química General e Inorgánica, CABA, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Bioquímica y Medicina Molecular (IBIMOL), Buenos Aires, CABA, Argentina
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Toker L, Nido GS, Tzoulis C. Not every estimate counts - evaluation of cell composition estimation approaches in brain bulk tissue data. Genome Med 2023; 15:41. [PMID: 37287013 DOI: 10.1186/s13073-023-01195-2] [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: 01/15/2023] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND Variation in cell composition can dramatically impact analyses in bulk tissue samples. A commonly employed approach to mitigate this issue is to adjust statistical models using estimates of cell abundance derived directly from omics data. While an arsenal of estimation methods exists, the applicability of these methods to brain tissue data and whether or not cell estimates can sufficiently account for confounding cellular composition has not been adequately assessed. METHODS We assessed the correspondence between different estimation methods based on transcriptomic (RNA sequencing, RNA-seq) and epigenomic (DNA methylation and histone acetylation) data from brain tissue samples of 49 individuals. We further evaluated the impact of different estimation approaches on the analysis of H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-seq) data from entorhinal cortex of individuals with Alzheimer's disease and controls. RESULTS We show that even closely adjacent tissue samples from the same Brodmann area vary greatly in their cell composition. Comparison across different estimation methods indicates that while different estimation methods applied to the same data produce highly similar outcomes, there is a surprisingly low concordance between estimates based on different omics data modalities. Alarmingly, we show that cell type estimates may not always sufficiently account for confounding variation in cell composition. CONCLUSIONS Our work indicates that cell composition estimation or direct quantification in one tissue sample should not be used as a proxy to the cellular composition of another tissue sample from the same brain region of an individual-even if the samples are directly adjacent. The highly similar outcomes observed among vastly different estimation methods, highlight the need for brain benchmark datasets and better validation approaches. Finally, unless validated through complementary experiments, the interpretation of analyses outcomes based on data confounded by cell composition should be done with great caution, and ideally avoided all together.
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Affiliation(s)
- Lilah Toker
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
| | - Gonzalo S Nido
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed Center of Excellence, Department of Neurology, Department of Clinical Medicine, Haukeland University Hospital, University of Bergen, 5021, Bergen, Norway.
- Department of Clinical Medicine, University of Bergen, Pb 7804, 5020, Bergen, Norway.
- K.G Jebsen Center for Translational Research in Parkinson's Disease, University of Bergen, Bergen, Norway.
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Guitton R, Nido GS, Tzoulis C. No evidence of extensive non-CpG methylation in mtDNA. Nucleic Acids Res 2022; 50:9190-9194. [PMID: 35979955 PMCID: PMC9458446 DOI: 10.1093/nar/gkac701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022] Open
Abstract
While most research suggests mitochondrial DNA (mtDNA) harbors low or no methylation, a few studies claim to report evidence of high-level methylation in the mtDNA. The reasons behind these contradictory results are likely to be methodological but remain largely unexplored. Here, we critically reanalyzed a recent study by Patil et al. (2019) reporting extensive methylation in human mtDNA in a non-CpG context. Our analyses refute the original findings and show that these do not reflect the biology of the tested samples, but rather stem from a combination of methodological and technical pitfalls. The authors employ an oversimplified model that defines as methylated all reference positions with methylation proportions above an arbitrary cutoff of 9%. This substantially exacerbates the overestimation of methylated cytosines due to the selective degradation of unmethylated cytosine-rich regions. Additional limitations are the small sample sizes and lack of sample-specific controls for bisulfite conversion efficiency. In conclusion, using the same dataset employed in the original study by Patil et al., we find no evidence supporting the existence of extensive non-CpG methylation in the human mtDNA.
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Affiliation(s)
- Romain Guitton
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway,Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Gonzalo S Nido
- Correspondence may also be addressed to Gonzalo S. Nido. Tel: +47 55975061;
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Huang CH, Chang MC, Lai YC, Lin CY, Hsu CH, Tseng BY, Hsiao CK, Lu TP, Yu SL, Hsieh ST, Chen WJ. Mitochondrial DNA methylation profiling of the human prefrontal cortex and nucleus accumbens: correlations with aging and drug use. Clin Epigenetics 2022; 14:79. [PMID: 35752846 PMCID: PMC9233363 DOI: 10.1186/s13148-022-01300-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the brain's high demand for energy, research on its epigenetics focuses on nuclear methylation, and much of the mitochondrial DNA methylation remains seldom investigated. With a focus on the nucleus accumbens (NAcc) and the prefrontal cortex (PFC), we aimed to identify the mitochondrial methylation signatures for (1) distinguishing the two brain areas, (2) correlating with aging, and (3) reflecting the influence of illicit drugs on the brain. RESULT We collected the brain tissue in the NAcc and the PFC from the deceased individuals without (n = 39) and with (n = 14) drug use and used whole-genome bisulfite sequencing to cover cytosine sites in the mitochondrial genome. We first detected differential methylations between the NAcc and the PFC in the nonusers group (P = 3.89 × 10-9). These function-related methylation differences diminished in the drug use group due to the selective alteration in the NAcc. Then, we found the correlation between the methylation levels and the chronological ages in the nonusers group (R2 = 0.34 in the NAcc and 0.37 in the PFC). The epigenetic clocks in illicit drug users, especially in the ketamine users, were accelerated in both brain regions by comparison with the nonusers. Finally, we summarized the effect of the illicit drugs on the methylation, which could significantly differentiate the drug users from the nonusers (AUC = 0.88 in the NAcc, AUC = 0.94 in the PFC). CONCLUSION The mitochondrial methylations were different between different brain areas, generally accumulated with aging, and sensitive to the effects of illicit drugs. We believed this is the first report to elucidate comprehensively the importance of mitochondrial DNA methylation in human brain.
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Affiliation(s)
- Chia-Hung Huang
- Forensic Biology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan.,Forensic Pathology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan.,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Man-Chen Chang
- Forensic Biology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Yung-Chun Lai
- Forensic Biology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Chun-Yen Lin
- Forensic Biology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Cho-Hsien Hsu
- Forensic Pathology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Bo-Yuan Tseng
- Forensic Pathology Division, Institute of Forensic Medicine, Ministry of Justice, New Taipei City, Taiwan
| | - Chuhsing Kate Hsiao
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Tsang Hsieh
- Department of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Neurology, College of Medicine and National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Wei J Chen
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan. .,Department of Psychiatry, College of Medicine and National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan. .,Center for Neuropsychiatric Research, National Health Research Institutes, Zhunan, Miaoli County, Taiwan.
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