Login Register Cart 0
Generic placeholder image

Current Molecular Medicine

Editor-in-Chief

ISSN (Print): 1566-5240
ISSN (Online): 1875-5666

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe Translate in Chinese
Research Article

A New Approach to Identify the Methylation Sites in the Control Region of Mitochondrial DNA

Author(s): Ashael Alfredo Pérez-Muñoz, María de Lourdes Muñoz*, Normand García-Hernández* and Heriberto Santander-Lucio

Volume 21, Issue 2, 2021

Published on: 28 May, 2020

Page: [151 - 164] Pages: 14

DOI: 10.2174/1566524020666200528154005

Price: $65

Abstract

Mitochondrial DNA (mtDNA) methylation has the potential to be used as a biomarker of human development or disease. However, mtDNA methylation procedures are costly and time-consuming. Therefore, we developed a new approach based on an RT-PCR assay for the base site identification of methylated cytosine in the control region of mtDNA through a simple, fast, specific, and low-cost strategy. Total DNA was purified, and methylation was determined by RT-PCR bisulfite sequencing. This procedure included the DNA purification, bisulfite treatment and RT-PCR amplification of the control region divided into three subregions with specific primers. Sequences obtained with and without the bisulfite treatment were compared to identify the methylated cytosine dinucleotides. Furthermore, the efficiency of C to U conversion of cytosines was assessed by including a negative control. Interestingly, mtDNA methylation was observed mainly within non-Cphosphate- G (non-CpG) dinucleotides and mostly in the regions containing regulatory elements, such as OH or CSBI, CSBII, and CSBIII. This new approach will promote the generation of new information regarding mtDNA methylation patterns in samples from patients with different pathologies or that are exposed to a toxic environment in diverse human populations.

Keywords: Mitochondrial epigenetics, bisulfite sequencing, methylation, mitochondrial DNA, D-loop, RT-PCR.

« Previous Next »
[1]
Grivell LA, Mitochondrial DNA. Small, beautiful and essential. Nature 1989; 341(6243): 569-71.
[http://dx.doi.org/10.1038/341569a0] [PMID: 2797187]
[2]
Grzybowska-Szatkowska L, Slaska B. Mitochondrial NADH dehydrogenase polymorphisms are associated with breast cancer in Poland. J Appl Genet 2014; 55(2): 173-81.
[http://dx.doi.org/10.1007/s13353-013-0190-9] [PMID: 24414975]
[3]
Rebelo AP, Dillon LM, Moraes CT. Mitochondrial DNA transcription regulation and nucleoid organization. J Inherit Metab Dis 2011; 34(4): 941-51.
[http://dx.doi.org/10.1007/s10545-011-9330-8] [PMID: 21541724]
[4]
Gilkerson R, Bravo L, Garcia I, et al. The mitochondrial nucleoid: integrating mitochondrial DNA into cellular homeostasis. Cold Spring Harb Perspect Biol 2013; 5(5)a011080
[http://dx.doi.org/10.1101/cshperspect.a011080] [PMID: 23637282]
[5]
Raule N, Sevini F, Li S, et al. The co-occurrence of mtDNA mutations on different oxidative phosphorylation subunits, not detected by haplogroup analysis, affects human longevity and is population specific. Aging Cell 2014; 13(3): 401-7.
[http://dx.doi.org/10.1111/acel.12186] [PMID: 24341918]
[6]
Schon EA, DiMauro S, Hirano M. Human mitochondrial DNA: roles of inherited and somatic mutations. Nat Rev Genet 2012; 13(12): 878-90.
[http://dx.doi.org/10.1038/nrg3275] [PMID: 23154810]
[7]
Hudson G, Gomez-Duran A, Wilson IJ, Chinnery PF. Recent mitochondrial DNA mutations increase the risk of developing common late-onset human diseases. PLoS Genet 2014; 10(5)e1004369
[http://dx.doi.org/10.1371/journal.pgen.1004369] [PMID: 24852434]
[8]
Dowling DK. Evolutionary perspectives on the links between mitochondrial genotype and disease phenotype. Biochim Biophys Acta 2014; 1840(4): 1393-403.
[http://dx.doi.org/10.1016/j.bbagen.2013.11.013] [PMID: 24246955]
[9]
Mposhi A, Van der Wijst MG, Faber KN, Rots MG. Regulation of mitochondrial gene expression, the epigenetic enigma. Front Biosci 2017; 22: 1099-113.
[http://dx.doi.org/10.2741/4535] [PMID: 28199194]
[10]
D’Aquila P, Bellizzi D, Passarino G. Mitochondria in health, aging and diseases: the epigenetic perspective. Biogerontology 2015; 16(5): 569-85.
[http://dx.doi.org/10.1007/s10522-015-9562-3] [PMID: 25711915]
[11]
Behzad MM, Shahrabi S, Jaseb K, Bertacchini J, Ketabchi N, Saki N. Aberrant DNA Methylation in Chronic Myeloid Leukemia: Cell Fate Control, Prognosis, and Therapeutic Response. Biochem Genet 2018; 56(3): 149-75.
[http://dx.doi.org/10.1007/s10528-018-9841-1] [PMID: 29388070]
[12]
Liu Y, Tan Q, Liu F. Differentially methylated circulating DNA: A novel biomarker to monitor beta cell death. J Diabetes Complications 2018; 32(3): 349-53.
[http://dx.doi.org/10.1016/j.jdiacomp.2017.08.012] [PMID: 29415820]
[13]
Xin Y, O’Donnell AH, Ge Y, et al. Role of CpG context and content in evolutionary signatures of brain DNA methylation. Epigenetics 2011; 6(11): 1308-18.
[http://dx.doi.org/10.4161/epi.6.11.17876] [PMID: 22048252]
[14]
Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 2006; 103(5): 1412-7.
[http://dx.doi.org/10.1073/pnas.0510310103] [PMID: 16432200]
[15]
Iacobazzi V, Castegna A, Infantino V, Andria G. Mitochondrial DNA methylation as a next-generation biomarker and diagnostic tool. Mol Genet Metab 2013; 110(1-2): 25-34.
[http://dx.doi.org/10.1016/j.ymgme.2013.07.012] [PMID: 23920043]
[16]
Bellizzi D, D’Aquila P, Scafone T, et al. The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern. DNA Res 2013; 20(6): 537-47.
[http://dx.doi.org/10.1093/dnares/dst029] [PMID: 23804556]
[17]
Bianchessi V, Vinci MC, Nigro P, et al. Methylation profiling by bisulfite sequencing analysis of the mtDNA Non-Coding Region in replicative and senescent Endothelial Cells. Mitochondrion 2016; 27: 40-7.
[http://dx.doi.org/10.1016/j.mito.2016.02.004] [PMID: 26910457]
[18]
Saini SK, Mangalhara KC, Prakasam G, Bamezai RNK. DNA Methyltransferase1 (DNMT1) Isoform3 methylates mitochondrial genome and modulates its biology. Sci Rep 2017; 7(1): 1525.
[http://dx.doi.org/10.1038/s41598-017-01743-y] [PMID: 28484249]
[19]
Gowher H, Jeltsch A. Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpG [correction of non-CpA] sites. J Mol Biol 2001; 309(5): 1201-8.
[http://dx.doi.org/10.1006/jmbi.2001.4710] [PMID: 11399089]
[20]
Yu D, Du Z, Pian L, et al. Mitochondrial DNA Hypomethylation Is a Biomarker Associated with Induced Senescence in Human Fetal Heart Mesenchymal Stem Cells. Stem Cells Int 2017.20171764549
[http://dx.doi.org/10.1155/2017/1764549] [PMID: 28484495]
[21]
Jia Y, Song H, Gao G, Cai D, Yang X, Zhao R. Maternal Betaine Supplementation during Gestation Enhances Expression of mtDNA-Encoded Genes through D-Loop DNA Hypomethylation in the Skeletal Muscle of Newborn Piglets. J Agric Food Chem 2015; 63(46): 10152-60.
[http://dx.doi.org/10.1021/acs.jafc.5b04418] [PMID: 26527363]
[22]
Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 2012; 13(7): 484-92.
[http://dx.doi.org/10.1038/nrg3230] [PMID: 22641018]
[23]
Byun HM, Panni T, Motta V, et al. Effects of airborne pollutants on mitochondrial DNA methylation. Part Fibre Toxicol 2013; 10: 18.
[http://dx.doi.org/10.1186/1743-8977-10-18] [PMID: 23656717]
[24]
Pirola CJ, Gianotti TF, Burgueño AL, et al. Epigenetic modification of liver mitochondrial DNA is associated with histological severity of nonalcoholic fatty liver disease. Gut 2013; 62(9): 1356-63.
[http://dx.doi.org/10.1136/gutjnl-2012-302962] [PMID: 22879518]
[25]
Blanch M, Mosquera JL, Ansoleaga B, Ferrer I, Barrachina M. Altered Mitochondrial DNA Methylation Pattern in Alzheimer Disease-Related Pathology and in Parkinson Disease. Am J Pathol 2016; 186(2): 385-97.
[http://dx.doi.org/10.1016/j.ajpath.2015.10.004] [PMID: 26776077]
[26]
Devall M, Mill J, Lunnon K. The mitochondrial epigenome: a role in Alzheimer’s disease? Epigenomics 2014; 6(6): 665-75.
[http://dx.doi.org/10.2217/epi.14.50] [PMID: 25531259]
[27]
Mishra M, Kowluru RA. Epigenetic Modification of Mitochondrial DNA in the Development of Diabetic Retinopathy. Invest Ophthalmol Vis Sci 2015; 56(9): 5133-42.
[http://dx.doi.org/10.1167/iovs.15-16937] [PMID: 26241401]
[28]
Taylor RW, Taylor GA, Durham SE, Turnbull DM. The determination of complete human mitochondrial DNA sequences in single cells: implications for the study of somatic mitochondrial DNA point mutations. Nucleic Acids Res 2001; 29(15): E74-4.
[http://dx.doi.org/10.1093/nar/29.15.e74] [PMID: 11470889]
[29]
Kumar S, Bellis C, Zlojutro M, Melton PE, Blangero J, Curran JE. Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evol Biol 2011; 11: 293.
[http://dx.doi.org/10.1186/1471-2148-11-293] [PMID: 21978175]
[30]
Lott MT, Leipzig JN, Derbeneva O, et al. Wallace, mtDNA Variation and Analysis Using Mitomap and Mitomaster Curr Protoc Bioinformatics 2013 44: 1 23-1-26.
[31]
Matsuda S, Yasukawa T, Sakaguchi Y, et al. Accurate estimation of 5-methylcytosine in mammalian mitochondrial DNA. Sci Rep 2018; 8(1): 5801.
[http://dx.doi.org/10.1038/s41598-018-24251-z] [PMID: 29643477]
[32]
Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology 2013; 38(1): 23-38.
[http://dx.doi.org/10.1038/npp.2012.112] [PMID: 22781841]
[33]
Lioznova AV, Khamis AM, Artemov AV, et al. CpG traffic lights are markers of regulatory regions in human genome. BMC Genomics 2019; 20(1): 102.
[http://dx.doi.org/10.1186/s12864-018-5387-1] [PMID: 30709331]
[34]
Jin B, Li Y, Robertson KD. DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer 2011; 2(6): 607-17.
[http://dx.doi.org/10.1177/1947601910393957] [PMID: 21941617]
[35]
Hanna CW, Demond H, Kelsey G. Epigenetic regulation in development: is the mouse a good model for the human? Hum Reprod Update 2018; 24(5): 556-76.
[http://dx.doi.org/10.1093/humupd/dmy021] [PMID: 29992283]
[36]
Rose NR, Klose RJ. Understanding the relationship between DNA methylation and histone lysine methylation. Biochim Biophys Acta 2014; 1839(12): 1362-72.
[http://dx.doi.org/10.1016/j.bbagrm.2014.02.007] [PMID: 24560929]
[37]
Ficz G. New insights into mechanisms that regulate DNA methylation patterning. J Exp Biol 2015; 218(Pt 1): 14-20.
[http://dx.doi.org/10.1242/jeb.107961] [PMID: 25568447]
[38]
Raine A, Liljedahl U, Nordlund J. Data quality of whole genome bisulfite sequencing on Illumina platforms. PLoS One 2018; 13(4)e0195972
[http://dx.doi.org/10.1371/journal.pone.0195972] [PMID: 29668744]
[39]
Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 2015; 10(3): 475-83.
[http://dx.doi.org/10.1038/nprot.2014.114] [PMID: 25692984]
[40]
Mechta M, Ingerslev LR, Fabre O, Picard M, Barrès R. Evidence Suggesting Absence of Mitochondrial DNA Methylation. Front Genet 2017; 8: 166.
[http://dx.doi.org/10.3389/fgene.2017.00166] [PMID: 29163634]
[41]
Abel ED. Mitochondrial Dynamics and Metabolic Regulation in Cardiac and Skeletal Muscle. Trans Am Clin Climatol Assoc 2018; 129: 266-78.
[PMID: 30166722]
[42]
Lundsgaard AM, Fritzen AM, Kiens B. Molecular Regulation of Fatty Acid Oxidation in Skeletal Muscle during Aerobic Exercise. Trends Endocrinol Metab 2018; 29(1): 18-30.
[http://dx.doi.org/10.1016/j.tem.2017.10.011] [PMID: 29221849]
[43]
Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 2008; 9(6): 465-76.
[http://dx.doi.org/10.1038/nrg2341] [PMID: 18463664]
[44]
Feng J, Zhou Y, Campbell SL, et al. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 2010; 13(4): 423-30.
[http://dx.doi.org/10.1038/nn.2514] [PMID: 20228804]
[45]
Pollack Y, Kasir J, Shemer R, Metzger S, Szyf M. Methylation pattern of mouse mitochondrial DNA. Nucleic Acids Res 1984; 12(12): 4811-24.
[http://dx.doi.org/10.1093/nar/12.12.4811] [PMID: 6330684]
[46]
Infantino V, Castegna A, Iacobazzi F, et al. Impairment of methyl cycle affects mitochondrial methyl availability and glutathione level in Down’s syndrome. Mol Genet Metab 2011; 102(3): 378-82.
[http://dx.doi.org/10.1016/j.ymgme.2010.11.166] [PMID: 21195648]
[47]
Shock LS, Thakkar PV, Peterson EJ, Moran RG, Taylor SM. DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proc Natl Acad Sci USA 2011; 108(9): 3630-5.
[http://dx.doi.org/10.1073/pnas.1012311108] [PMID: 21321201]
[48]
Ghosh S, Sengupta S, Scaria V. Hydroxymethyl cytosine marks in the human mitochondrial genome are dynamic in nature. Mitochondrion 2016; 27: 25-31.
[http://dx.doi.org/10.1016/j.mito.2016.01.003] [PMID: 26826294]
[49]
Kurdyukov S, Bullock M. DNA Methylation Analysis: Choosing the Right Method. Biology (Basel) 2016; 5(1)E3
[http://dx.doi.org/10.3390/biology5010003] [PMID: 26751487]
[50]
Morris J, Grimmer-Somers K, Kumar S, et al. Effectiveness of a physiotherapy-initiated telephone triage of orthopedic waitlist patients. Patient Relat Outcome Meas 2011; 2: 151-9.
[PMID: 22915976]
[51]
Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 2010; 5(1)e8888
[52]
Martinez-Cortes J, Salazar-Flores J, Haro-Guerrero R, et al. Maternal admixture and population structure in Mexican-Mestizos based on mtDNA haplogroups. Am J Phys Anthropol 2013; 151(4): 526-37.
[PMID: 23754474]
[53]
Patil V, Cuenin C, Chung F, et al. Human mitochondrial DNA is extensively methylated in a non-CpG context. Nucleic Acids Res 2019; 47(19): 10072-85.
[http://dx.doi.org/10.1093/nar/gkz762] [PMID: 31665742]
[54]
Cardon LR, Burge C, Clayton DA, Karlin S. Pervasive CpG suppression in animal mitochondrial genomes. Proc Natl Acad Sci USA 1994; 91(9): 3799-803.
[http://dx.doi.org/10.1073/pnas.91.9.3799] [PMID: 8170990]
[55]
Guo JU, Su Y, Shin JH, et al. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat Neurosci 2014; 17(2): 215-22.
[http://dx.doi.org/10.1038/nn.3607] [PMID: 24362762]
[56]
Grandjean V, Yaman R, Cuzin F, Rassoulzadegan M. Inheritance of an epigenetic mark: the CpG DNA methyltransferase 1 is required for de novo establishment of a complex pattern of non-CpG methylation. PLoS One 2007; 2(11)e1136
[http://dx.doi.org/10.1371/journal.pone.0001136] [PMID: 17989773]
[57]
Wong M, Gertz B, Chestnut BA, Martin LJ. Mitochondrial DNMT3A and DNA methylation in skeletal muscle and CNS of transgenic mouse models of ALS. Front Cell Neurosci 2013; 7: 279.
[http://dx.doi.org/10.3389/fncel.2013.00279] [PMID: 24399935]
[58]
Denis H, Ndlovu MN, Fuks F. Regulation of mammalian DNA methyltransferases: a route to new mechanisms. EMBO Rep 2011; 12(7): 647-56.
[http://dx.doi.org/10.1038/embor.2011.110] [PMID: 21660058]
[59]
Harte AL, Varma MC, Tripathi G, et al. High fat intake leads to acute postprandial exposure to circulating endotoxin in type 2 diabetic subjects. Diabetes Care 2012; 35(2): 375-82.
[http://dx.doi.org/10.2337/dc11-1593] [PMID: 22210577]
[60]
Nicholls TJ, Minczuk M. In D-loop: 40 years of mitochondrial 7S DNA. Exp Gerontol 2014; 56: 175-81.
[http://dx.doi.org/10.1016/j.exger.2014.03.027] [PMID: 24709344]
[61]
Kim JA, Kwon M, Kim J. Allosteric Regulation of Chromatin-Modifying Enzymes. Biochemistry 2018.
[PMID: 30335997]

Rights & Permissions Print Cite
Article Metrics
30
1
World Malaria Day
© 2024 Bentham Science Publishers | Privacy Policy