1
|
O’Brown ZK, Greer EL. N6-methyladenine: A Rare and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:177-210. [DOI: 10.1007/978-3-031-11454-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
2
|
Kim CH, Lee EK, Choi YJ, An HJ, Jeong HO, Park D, Kim BC, Yu BP, Bhak J, Chung HY. Short-term calorie restriction ameliorates genomewide, age-related alterations in DNA methylation. Aging Cell 2016; 15:1074-1081. [PMID: 27561685 PMCID: PMC6398531 DOI: 10.1111/acel.12513] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2016] [Indexed: 01/14/2023] Open
Abstract
DNA methylation plays major roles in many biological processes, including aging, carcinogenesis, and development. Analyses of DNA methylation using next-generation sequencing offer a new way to profile and compare methylomes across the genome in the context of aging. We explored genomewide DNA methylation and the effects of short-term calorie restriction (CR) on the methylome of aged rat kidney. Whole-genome methylation of kidney in young (6 months old), old (25 months old), and OCR (old with 4-week, short-term CR) rats was analyzed by methylated DNA immunoprecipitation and next-generation sequencing (MeDIP-Seq). CpG islands and repetitive regions were hypomethylated, but 5'-UTR, exon, and 3'-UTR hypermethylated in old and OCR rats. The methylation in the promoter and intron regions was decreased in old rats, but increased in OCR rats. Pathway enrichment analysis showed that the hypermethylated promoters in old rats were associated with degenerative phenotypes such as cancer and diabetes. The hypomethylated promoters in old rats related significantly to the chemokine signaling pathway. However, the pathways significantly enriched in old rats were not observed from the differentially methylated promoters in OCR rats. Thus, these findings suggest that short-term CR could partially ameliorate age-related methylation changes in promoters in old rats. From the epigenomic data, we propose that the hypermethylation found in the promoter regions of disease-related genes during aging may indicate increases in susceptibility to age-related diseases. Therefore, the CR-induced epigenetic changes that ameliorate age-dependent aberrant methylation may be important to CR's health- and life-prolonging effects.
Collapse
Affiliation(s)
| | - Eun Kyeong Lee
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Yeon Ja Choi
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Hye Jin An
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Hyeong Oh Jeong
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| | - Daeui Park
- Department of Predictive Toxicology Korea Institute of Toxicology Daejeon Korea
| | - Byoung Chul Kim
- Department of Predictive Toxicology Korea Institute of Toxicology Daejeon Korea
| | - Byung Pal Yu
- Department of Physiology University of Texas Health Science Center San Antonio TX USA
| | - Jong Bhak
- Biomedical Engineering Ulsan National Institute of Sciences and Technology Ulsan Korea
| | - Hae Yung Chung
- Molecular Inflammation Research Center for Aging Intervention (MRCA) College of Pharmacy Pusan National University Busan Republic of Korea
| |
Collapse
|
3
|
O'Brown ZK, Greer EL. N6-Methyladenine: A Conserved and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:213-246. [PMID: 27826841 DOI: 10.1007/978-3-319-43624-1_10] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Chromatin, consisting of deoxyribonucleic acid (DNA) wrapped around histone proteins, facilitates DNA compaction and allows identical DNA codes to confer many different cellular phenotypes. This biological versatility is accomplished in large part by posttranslational modifications to histones and chemical modifications to DNA. These modifications direct the cellular machinery to expand or compact specific chromatin regions and mark regions of the DNA as important for cellular functions. While each of the four bases that make up DNA can be modified (Iyer et al. 2011), this chapter will focus on methylation of the sixth position on adenines (6mA), as this modification has been poorly characterized in recently evolved eukaryotes, but shows promise as a new conserved layer of epigenetic regulation. 6mA was previously thought to be restricted to unicellular organisms, but recent work has revealed its presence in metazoa. Here, we will briefly describe the history of 6mA, examine its evolutionary conservation, and evaluate the current methods for detecting 6mA. We will discuss the enzymes that bind and regulate this mark and finally examine known and potential functions of 6mA in eukaryotes.
Collapse
Affiliation(s)
- Zach Klapholz O'Brown
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric Lieberman Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
4
|
Ng JWY, Barrett LM, Wong A, Kuh D, Smith GD, Relton CL. The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities. Genome Biol 2012; 13:246. [PMID: 22747597 PMCID: PMC3446311 DOI: 10.1186/gb-2012-13-6-246] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Longitudinal cohort studies are ideal for investigating how epigenetic patterns change over time and relate to changing exposure patterns and the development of disease. We highlight the challenges and opportunities in this approach.
Collapse
|
5
|
Ng JWY, Barrett LM, Wong A, Kuh D, Smith G, Relton CL. The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities. Genome Biol 2012. [DOI: 10.1186/gb4029] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
|
6
|
|
7
|
Osorio FG, Varela I, Lara E, Puente XS, Espada J, Santoro R, Freije JMP, Fraga MF, López-Otín C. Nuclear envelope alterations generate an aging-like epigenetic pattern in mice deficient in Zmpste24 metalloprotease. Aging Cell 2010; 9:947-57. [PMID: 20961378 DOI: 10.1111/j.1474-9726.2010.00621.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mutations in the nuclear envelope protein lamin A or in its processing protease ZMPSTE24 cause human accelerated aging syndromes, including Hutchinson-Gilford progeria syndrome. Similarly, Zmpste24-deficient mice accumulate unprocessed prelamin A and develop multiple progeroid symptoms, thus representing a valuable animal model for the study of these syndromes. Zmpste24-deficient mice also show marked transcriptional alterations associated with chromatin disorganization, but the molecular links between both processes are unknown. We report herein that Zmpste24-deficient mice show a hypermethylation of rDNA that reduces the transcription of ribosomal genes, being this reduction reversible upon treatment with DNA methyltransferase inhibitors. This alteration has been previously described during physiological aging in rodents, suggesting its potential role in the development of the progeroid phenotypes. We also show that Zmpste24-deficient mice present global hypoacetylation of histones H2B and H4. By using a combination of RNA sequencing and chromatin immunoprecipitation assays, we demonstrate that these histone modifications are associated with changes in the expression of several genes involved in the control of cell proliferation and metabolic processes, which may contribute to the plethora of progeroid symptoms exhibited by Zmpste24-deficient mice. The identification of these altered genes may help to clarify the molecular mechanisms underlying aging and progeroid syndromes as well as to define new targets for the treatment of these dramatic diseases.
Collapse
Affiliation(s)
- Fernando G Osorio
- Departamento de Bioquímica y Biología Molecular Unidad de Epigenética, Instituto Universitario de Oncología, Universidad de Oviedo, 33006-Oviedo, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Lopes FL, Fortier AL, Darricarrère N, Chan D, Arnold DR, Trasler JM. Reproductive and epigenetic outcomes associated with aging mouse oocytes. Hum Mol Genet 2009; 18:2032-44. [DOI: 10.1093/hmg/ddp127] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
9
|
Abstract
Monozygotic twins share the same genotype because they are derived from the same zygote. However, monozygotic twin siblings frequently present many phenotypic differences, such as their susceptibility to disease and a wide range of anthropomorphic features. Recent studies suggest that phenotypic discordance between monozygotic twins is at least to some extent due to epigenetic factors that change over the lifetime of a multicellular organism. It has been proposed that epigenetic drift during development can be stochastic or determined by environmental factors. In reality, a combination of the two causes prevails in most cases. Acute environmental factors are directly associated with epigenetic-dependent disease phenotypes, as demonstrated by the increased CpG-island promoter hypermethylation of tumor suppressor genes in the normal oral mucosa of smokers. Since monozygotic twins are genetically identical they are considered ideal experimental models for studying the role of environmental factors as determinants of complex diseases and phenotypes.
Collapse
|
10
|
Abstract
Although there appear to be several influences, which contribute to the ageing of mammals, the role of DNA appears to be pivotal. There is increasing evidence that oxidative damage is an important factor in producing mutations in genes, shortening telomeres and damaging mitochondrial DNA. Accumulation of mutations in genomic DNA could result in the gradual decline in cellular function, which is exhibited in a variety of tissues. The random nature of these mutations, could also offer an explanation for differences in the degree and time of onset of age-related changes, exhibited by different individuals. Shortening of telomeres, caused by oxidative damage or the end-replication problem, could result in the accumulation of post-mitotic cells in-vivo during ageing. This might impair certain aspects of physiology, such as wound healing. Mutation of mitochondrial DNA may also be important in causing loss of cells in post-mitotic tissues such as muscle or brain. In addition changes in the redox state during the life of an animal may alter transcription factor activities, leading to consistent changes in the gene expression profiles of mammalian tissues. The latter could explain consistent age-related changes that have been observed in cell structure and physiology. Although all of these mechanisms may make a contribution to ageing, it is likely that it is the interplay between them that produces the most prominent effects.
Collapse
Affiliation(s)
- Malcolm H Goyns
- Molecular Gerontology Unit, School of Sciences, University of Sunderland, Fleming Building, Wharncliffe Street, SR1 3SD, Sunderland, UK.
| |
Collapse
|
11
|
DNA base modifications in aging. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1566-3124(01)04027-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
12
|
Tawa R, Takami M, Imakura Y, Lee KH, Sakurai H. Effects of CpG methylation to double stranded DNA breaks by Cu(II)-podophyllotoxin derivative complexes. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00015-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
13
|
Abstract
Progress in molecular biological investigations of aging in Japan is overviewed. Emphasis is put on studies which, in the author's opinion, appear to have considerable relevance to a definition of aging, i.e. functional decline of cells and tissues with advancing age. (1) Changes in the nuclear DNA, most significantly in methylation, and deletions of mitochondrial DNA have been shown to occur with age. (2) Various aspects of protein metabolism have been investigated, i.e. the fidelity of translation, accumulation of altered enzymes, oxidative damage, and half-lives and degradation of proteins. (3) Japanese researchers have made significant contributions to the understanding of the chemical structure and the mechanisms of generation of paired helical filaments in Alzheimer's disease. Also, studies on beta-amyloid peptide are noteworthy. (4) Murine models of aging were developed and molecular biological investigations on them are progressing. Nematodes and fruit flies are also used as models.(5) Changes in gene expression with age have attracted considerable interest.
Collapse
Affiliation(s)
- S Goto
- Department of Biochemistry, School of Pharmaceutical Sciences, Toho University, Miyama, Funabashi, Chiba, 274, Japan
| |
Collapse
|
14
|
Tawa R, Tamura G, Sakurai H, Ono T, Kurishita A. High-performance liquid chromatographic analysis of methylation changes of CCGG sequence in brain and liver DNA of mice during pre- and postnatal development. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL APPLICATIONS 1994; 653:211-6. [PMID: 8205248 DOI: 10.1016/0378-4347(93)e0421-l] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The change of the methylation of CpG in the CCGG sequence of brain and liver DNAs of mice during late fetal and suckling periods was determined by high-performance liquid chromatography using a reversed-phase column and 0.1 M phosphate buffer (pH 6.0) as the mobile phase. The tissue DNA was digested with the restriction enzyme, MspI, and was labeled at the 5'-end with [gamma-32P]ATP. The cpm% of deoxycytidine 5'-monophosphate (5mdCMP) in total CpG dinucleotides was calculated from the equation 5mdCMP/total CCGG (cpm%) = (5mdCMP)MspI,cpm/[(5mdCMP)MspI,cpm + (dCMP)MspI,cpm] x 100. The brain DNA exhibited a significant decrease in CpG methylation at prenatal day 18 but little change after birth. This marked decline of 5mdCMP in the CCGG sequence may be associated with the increase of enzymes before birth. The liver DNA showed considerable change during the late prenatal period. The observed changes of CpG methylation in liver DNA are indicative of the corresponding alterations of enzymes, multinucleate cells and hepatocytes. The results obtained indicate that both brain and liver cells have the development-associated changes in the conformation and transition of DNA around the time of birth.
Collapse
Affiliation(s)
- R Tawa
- Department of Analytical Chemistry I, Kyoto Pharmaceutical University, Japan
| | | | | | | | | |
Collapse
|
15
|
Miyamura Y, Tawa R, Koizumi A, Uehara Y, Kurishita A, Sakurai H, Kamiyama S, Ono T. Effects of energy restriction on age-associated changes of DNA methylation in mouse liver. Mutat Res 1993; 295:63-9. [PMID: 7680421 DOI: 10.1016/0921-8734(93)90002-k] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
DNA methylation is known to change with age in several mammalian species. Here we have examined the effect of dietary energy restriction on this age-associated change in liver DNA of C3H/SHN mice. The total 5-methyldeoxycytidine level in the genome decreased slightly soon after energy restriction started. The effect, however, diminished with time and no appreciable difference was detected at middle and old ages. The degree of methylation at the c-myc gene, on the other hand, was not affected by energy restriction at early periods, but the age-dependent alterations at later ages were repressed. This is a new finding to show that DNA methylation is one of the molecular indices of aging affected by energy restriction. It suggests an importance of DNA methylation in the aging process.
Collapse
Affiliation(s)
- Y Miyamura
- Department of Radiation Research, Tohoku University School of Medicine, Sendai, Japan
| | | | | | | | | | | | | | | |
Collapse
|