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Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel) 2018; 9:genes9110566. [PMID: 30469440 PMCID: PMC6266221 DOI: 10.3390/genes9110566] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. After summarizing the impact of DNA methylation on genome evolution including CpG depletion, we describe the connection of DNA methylation with several important histone post-translational modifications, including methylation of H3K4, H3K9, H3K27, and H3K36, but also with nucleosome remodeling. Moreover, we present the mechanistic features of mammalian DNA methyltransferases and their associated factors that mediate the crosstalk between DNA methylation and chromatin modifications. Finally, we describe recent advances regarding the methylation of non-CpG sites, methylation of adenine residues in human cells and methylation of mitochondrial DNA. At several places, we highlight controversial findings or open questions demanding future experimental work.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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Saini SK, Kalaiarasan P, Singh RK, Manvati S, Bamezai R. MicroRNA (hsa-miR-19b-2-5p) targets key mitochondrial biogenesis genes-a bioinformatics analysis. Mitochondrion 2018; 43:30-36. [DOI: 10.1016/j.mito.2018.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 01/06/2023]
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53
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Onyango AN. Cellular Stresses and Stress Responses in the Pathogenesis of Insulin Resistance. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:4321714. [PMID: 30116482 PMCID: PMC6079365 DOI: 10.1155/2018/4321714] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 02/18/2018] [Indexed: 12/14/2022]
Abstract
Insulin resistance (IR), a key component of the metabolic syndrome, precedes the development of diabetes, cardiovascular disease, and Alzheimer's disease. Its etiological pathways are not well defined, although many contributory mechanisms have been established. This article summarizes such mechanisms into the hypothesis that factors like nutrient overload, physical inactivity, hypoxia, psychological stress, and environmental pollutants induce a network of cellular stresses, stress responses, and stress response dysregulations that jointly inhibit insulin signaling in insulin target cells including endothelial cells, hepatocytes, myocytes, hypothalamic neurons, and adipocytes. The insulin resistance-inducing cellular stresses include oxidative, nitrosative, carbonyl/electrophilic, genotoxic, and endoplasmic reticulum stresses; the stress responses include the ubiquitin-proteasome pathway, the DNA damage response, the unfolded protein response, apoptosis, inflammasome activation, and pyroptosis, while the dysregulated responses include the heat shock response, autophagy, and nuclear factor erythroid-2-related factor 2 signaling. Insulin target cells also produce metabolites that exacerbate cellular stress generation both locally and systemically, partly through recruitment and activation of myeloid cells which sustain a state of chronic inflammation. Thus, insulin resistance may be prevented or attenuated by multiple approaches targeting the different cellular stresses and stress responses.
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Affiliation(s)
- Arnold N. Onyango
- Department of Food Science and Technology, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi 00200, Kenya
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54
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Kim SJ, Mehta HH, Wan J, Kuehnemann C, Chen J, Hu JF, Hoffman AR, Cohen P. Mitochondrial peptides modulate mitochondrial function during cellular senescence. Aging (Albany NY) 2018; 10:1239-1256. [PMID: 29886458 PMCID: PMC6046248 DOI: 10.18632/aging.101463] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/30/2018] [Indexed: 12/31/2022]
Abstract
Cellular senescence is a complex cell fate response that is thought to underlie several age-related pathologies. Despite a loss of proliferative potential, senescent cells are metabolically active and produce energy-consuming effectors, including senescence-associated secretory phenotypes (SASPs). Mitochondria play crucial roles in energy production and cellular signaling, but the key features of mitochondrial physiology and particularly of mitochondria-derived peptides (MDPs), remain underexplored in senescence responses. Here, we used primary human fibroblasts made senescent by replicative exhaustion, doxorubicin or hydrogen peroxide treatment, and examined the number of mitochondria and the levels of mitochondrial respiration, mitochondrial DNA methylation and the mitochondria-encoded peptides humanin, MOTS-c, SHLP2 and SHLP6. Senescent cells showed increased numbers of mitochondria and higher levels of mitochondrial respiration, variable changes in mitochondrial DNA methylation, and elevated levels of humanin and MOTS-c. Humanin and MOTS-c administration modestly increased mitochondrial respiration and selected components of the SASP in doxorubicin-induced senescent cells partially via JAK pathway. Targeting metabolism in senescence cells is an important strategy to reduce SASP production for eliminating the deleterious effects of senescence. These results provide insight into the role of MDPs in mitochondrial energetics and the production of SASP components by senescent cells.
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Affiliation(s)
- Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Hemal H. Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Junxiang Wan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Jingcheng Chen
- Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA 94304, USA
| | - Andrew R. Hoffman
- Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, CA 94304, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
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55
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Accurate estimation of 5-methylcytosine in mammalian mitochondrial DNA. Sci Rep 2018; 8:5801. [PMID: 29643477 PMCID: PMC5895755 DOI: 10.1038/s41598-018-24251-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/28/2018] [Indexed: 02/06/2023] Open
Abstract
Whilst 5-methylcytosine (5mC) is a major epigenetic mark in the nuclear DNA in mammals, whether or not mitochondrial DNA (mtDNA) receives 5mC modification remains controversial. Herein, we exhaustively analysed mouse mtDNA using three methods that are based upon different principles for detecting 5mC. Next-generation bisulfite sequencing did not give any significant signatures of methylation in mtDNAs of liver, brain and embryonic stem cells (ESCs). Also, treatment with methylated cytosine-sensitive endonuclease McrBC resulted in no substantial decrease of mtDNA band intensities in Southern hybridisation. Furthermore, mass spectrometric nucleoside analyses of highly purified liver mtDNA preparations did not detect 5-methyldeoxycytidine at the levels found in the nuclear DNA but at a range of only 0.3-0.5% of deoxycytidine. Taken together, we propose that 5mC is not present at any specific region(s) of mtDNA and that levels of the methylated cytosine are fairly low, provided the modification occurs. It is thus unlikely that 5mC plays a universal role in mtDNA gene expression or mitochondrial metabolism.
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Shock L, Burton E, Robinson J, Taylor S. mtDNMT1 and DNMT3b cooperate to methylate mitochondrial DNA and regulate mitochondrial transcription. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.543.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lisa Shock
- Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVA
| | - Elliot Burton
- Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVA
| | - Jason Robinson
- Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVA
| | - Shirley Taylor
- Microbiology and ImmunologyVirginia Commonwealth UniversityRichmondVA
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Grayson DR, Guidotti A. DNA Methylation in Animal Models of Psychosis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:105-132. [PMID: 29933947 DOI: 10.1016/bs.pmbts.2017.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Schizophrenia (SZ) is a debilitating disease that impacts 1% of the population worldwide. Association studies have shown that inherited genetic mutations account for a portion of disease risk. However, environmental factors play an important role in the pathophysiology of the disease by altering cellular epigenetic marks at the level of chromatin. Postmortem brain studies of SZ subjects suggest that the dynamic equilibrium between DNA methylation and demethylation network components is disrupted at the level of individual SZ target genes. Herein, we review the role of DNA methylation and demethylation in the context of what is currently known regarding SZ. Furthermore, we describe the deficits that accompany two mouse models of SZ. The chronic methionine mouse model of SZ is predicated on the administration of methionine to SZ patients and controls in the context of clinical studies that were carried out during the 1960s and 1970s. The prenatal restraint stress model of SZ is based on a prolonged stress paradigm administered to pregnant dams during gestation days 7-21. The adult offspring of these dams show various behavioral and biochemical deficits in adulthood. Both models are epigenetic in origin and mimic the positive and negative symptoms, as well as the cognitive endophenotypes commonly observed in SZ patients. We also discuss the utility of typical and atypical antipsychotic drugs in alleviating these symptoms in each model.
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Affiliation(s)
- Dennis R Grayson
- Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States.
| | - Alessandro Guidotti
- Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States
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Sabharwal A, Sharma D, Vellarikkal SK, Jayarajan R, Verma A, Senthivel V, Scaria V, Sivasubbu S. Organellar transcriptome sequencing reveals mitochondrial localization of nuclear encoded transcripts. Mitochondrion 2018; 46:59-68. [PMID: 29486245 DOI: 10.1016/j.mito.2018.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/23/2018] [Accepted: 02/22/2018] [Indexed: 01/10/2023]
Abstract
Mitochondria are organelles involved in a variety of biological functions in the cell, apart from their principal role in generation of ATP, the cellular currency of energy. The mitochondria, in spite of being compact organelles, are capable of performing complex biological functions largely because of the ability to exchange proteins, RNA, chemical metabolites and other biomolecules between cellular compartments. A close network of biomolecular interactions are known to modulate the crosstalk between the mitochondria and the nuclear genome. Apart from the small repertoire of genes encoded by the mitochondrial genome, it is now known that the functionality of the organelle is highly reliant on a number of proteins encoded by the nuclear genome, which localize to the mitochondria. With exceptions to a few anecdotal examples, the transcripts that have the potential to localize to the mitochondria have been poorly studied. We used a deep sequencing approach to identify transcripts encoded by the nuclear genome which localize to the mitoplast in a zebrafish model. We prioritized 292 candidate transcripts of nuclear origin that are potentially localized to the mitochondrial matrix. We experimentally demonstrated that the transcript encoding the nuclear encoded ribosomal protein 11 (Rpl11) localizes to the mitochondria. This study represents a comprehensive analysis of the mitochondrial localization of nuclear encoded transcripts. Our analysis has provided insights into a new layer of biomolecular pathways modulating mitochondrial-nuclear cross-talk. This provides a starting point towards understanding the role of nuclear encoded transcripts that localize to mitochondria and their influence on mitochondrial function.
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Affiliation(s)
- Ankit Sabharwal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India
| | - Disha Sharma
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India
| | - Ankit Verma
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India
| | - Vigneshwar Senthivel
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India.
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mathura Road, Delhi 110 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus, Mathura Road, Delhi 110020, India.
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Ghosh S, Ranawat AS, Tolani P, Scaria V. Mitoepigenome KB a comprehensive resource for human mitochondrial epigenetic data. Mitochondrion 2017; 42:54-58. [PMID: 29129553 DOI: 10.1016/j.mito.2017.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/21/2017] [Accepted: 11/02/2017] [Indexed: 01/31/2023]
Abstract
Epigenetic modifications in the mitochondrial genome has been an emerging area of interest in the recent years in the field of mitochondrial biology. The renewed interest in the area has been largely fueled by a number of reports in the recent years suggesting the presence of epigenetic modifications in human mitochondrial genome and their associations with exposure to environmental factors and human diseases and or traits. Nevertheless there has been no systematic effort to curate, organize this information to enable cross-comparison between studies and datasets. We compiled 62 datasets from 9 studies on the epigenetic modifications in human mitochondrial genome to create a comprehensive catalog. This catalog is available as a user friendly interface - mitoepigenomeKB, where the data could be searched, browsed or visualized. The resource is available at URL: http://clingen.igib.res.in/mitoepigenome/. We hope mitoepigenomeKB would emerge as a central resource for datasets on epigenetic modifications in human mitochondria and would serve as the starting point to understanding the biology of human mitochondrial epigenome.
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Affiliation(s)
- Sourav Ghosh
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110 025, India
| | - Anop Singh Ranawat
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - Priya Tolani
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110 025, India.
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