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Handbook of Nutrition, Diet, and Epigenetics pp 529–547Cite as

Traces of Life’s Experiences: Epigenetics (DNA methylation) in Forensics

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Abstract

Since the development of methylation-based diagnostic biomarkers, the application of DNA methylation in forensic investigation is also rapidly gaining ground. DNA methylation patterns are established during early embryonic development and are influenced by both genetic and environmental factors like diet, age, stress, socioeconomic status, and habitat. Identification of differentially methylated regions (DMRs) which differ between tissues or phenotypes can be targeted for forensic applications. Tissue-specific methylation differences can be used for accurate identification of body fluid/ tissue source found at a crime scene. Age-specific methylation changes in repetitive genomic regions have been used to develop epigenetic clocks for age estimation. DNA methylation patterns differ even between monozygotic twins and can assist with the challenge of their identification. Recent development of whole genome methylation analysis platforms like Illumina whole genome methylation bead chips and single-cell reduced bisulfite sequencing has opened the doors for large-scale survey of methylation differences in both CpG islands and non-CpG regions. Future research could predict an individual’s social behavior and activities by applying DNA methylation indicators. Advancements in DNA methylation analysis for forensics will complement the current STR analysis and provide robust inferences for forensic evidence and human identification.

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Abbreviations

CpG:

Cytosine–phosphate–guanine

DmAM:

DNA methylation age measures

DMRs:

Differentially methylated regions

DNAm:

DNA methylation

DZ:

Dizygotic

ICR:

Imprinting control regions

LINE-1:

Long interspersed elements

MeCAP-seq:

Methylated DNA capture by affinity purification sequencing

MeDIP-seq:

Methylated DNA immunoprecipitation sequencing

MSRE-PCR:

Methylation-specific restriction enzyme polymerase chain reaction

MS-SNuPE:

Methylation-sensitive single-nucleotide primer extension

MZ:

Monozygotic

sjTRECs:

Signal joint TCR excision circles

SNP:

Single-nucleotide polymorphism

STR:

Simple sequence repeat

WGBS:

Whole genome bisulfite sequencing

References

  • Adkins RM, Krushkal J, Tylavsky FA, Thomas F (2011) Racial differences in gene-specific DNA methylation levels are present at birth. Birth Defects Res Part A Clin Mol Teratol 91:728–736

    Article  CAS  Google Scholar 

  • An JH, Choi A, Shin KJ et al (2013) DNA methylation specific multiplex assays for body fluid identification. Int J Legal Med 127:35

    Article  Google Scholar 

  • Bai L, Yan P, Cao X et al (2015) Methylation-sensitive restriction enzyme nested real time PCR, a potential approach for sperm DNA identification. J Forensic Legal Med 34:34–39

    Article  Google Scholar 

  • Barrett EL, Burke TA, Hammers M et al (2013) Telomere length and dynamics predict mortality in a wild longitudinal study. Mol Ecol 22:249–259

    Article  Google Scholar 

  • Bekaert B, Kamalandua A, Zapico S et al (2015) Improved age determination of blood and teeth samples using a selected set of DNA methylation markers. Epigenetics 10:922–930

    Article  Google Scholar 

  • Bennett DA, Yu L, Yang J et al (2015) Epigenomics of Alzheimer’s disease. Transl Res 165:200–220

    Article  CAS  Google Scholar 

  • Berdasco M, Esteller M (2012) Hot topics in epigenetic mechanisms of aging. Aging Cell 11:181–186

    Article  CAS  Google Scholar 

  • Bocklandt S, Lin W, Sehl ME et al (2011) Epigenetic predictor of age. PLoS One 22:e14821

    Article  Google Scholar 

  • Cappetta M, Berdasco M, Hochmann J et al (2015) Effect of genetic ancestry on leukocyte global DNA methylation in cancer patients. BMC Cancer 15:1

    Article  CAS  Google Scholar 

  • Castellani CA, Laufer BI, Melka MG et al (2015) DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks. BMC Med Genet 8(1):1

    CAS  Google Scholar 

  • Choi A, Shin KJ, Yang WI, Lee HY (2014) Body fluid identification by integrated analysis of DNA methylation and body fluid-specific microbial DNA. Int J Legal Med 128(1):33–41

    Article  Google Scholar 

  • Cordova-Palomera A, Fatjo-Vilas M, Gasto C et al (2015) Genome-wide methylation study on depression: differential methylation and variable methylation in monozygotic twins. Transl Psychiatry 5(4):e557

    Article  CAS  Google Scholar 

  • Craig JM (2010) Epigenetic studies of a newborn twin cohort: insights into prenatal development. Twin Res Hum Genet 13:252

    Google Scholar 

  • Dempster EL, Pidsley R, Schalkwyk LC et al (2011) Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder. Hum Mol Genet 20:4786–4796. https://doi.org/10.1093/hmg/ddr416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Du Q, Zhu G, Fu G et al (2015) A genome wide scan of DNA methylation markers for distinguishing monozygotic twins. Twin Res Hum Genet 18:670–679

    Article  Google Scholar 

  • Eckhardt F, Lewin J, Cortese R et al (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378–1385

    Article  CAS  Google Scholar 

  • Eriksson A, Manica A (2012) Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient Hominins. Proc Natl Acad Sci 109:13956–13960

    Article  CAS  Google Scholar 

  • Feng J, Zhou Y, Campbell SL et al (2010) Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13:423–430

    Article  CAS  Google Scholar 

  • Florath I, Butterbach K, Muller H et al (2014) Cross-sectional and longitudinal changes in DNA methylation with age: an epigenome-wide analysis revealing over 60 novel age-associated CpG sites. Hum Mol Genet 23:1186–1201

    Article  CAS  Google Scholar 

  • Forat S, Huettel B, Reinhardt R et al (2016) Methylation markers for the identification of body fluids and tissues from forensic trace evidence. PLoS One 11(2):e0147973

    Article  Google Scholar 

  • Fraga MF, Ballestar E, Paz MF, Ropero S et al (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A 102:10604–10609

    Article  CAS  Google Scholar 

  • Fraser HB, Lam LL, Neumann SM, Kobor MS (2012) Population-specificity of human DNA methylation. Genome Biol 13:1

    Article  Google Scholar 

  • Frumkin D, Wasserstrom A, Davidson A, Grafit A (2010) Authentication of forensic DNA samples. Forensic Sci Int Genet 4(2):95–103

    Article  CAS  Google Scholar 

  • Gunter TD (2015) Behavioral genetics and the forensic mental health provider: an overview. Behav Sci Law 33:598–606

    Article  Google Scholar 

  • Haas C, Hanson E, Anjos MJ et al (2014) RNA/DNA co-analysis from human menstrual blood and vaginal secretion stains: results of a fourth and fifth collaborative EDNAP exercise. Forensic Sci Int Genet 8(1):203–212

    Article  CAS  Google Scholar 

  • Hanson EK, Lubenow H, Ballantyne J (2009) Identification of forensically relevant body fluids using a panel of differentially expressed microRNAs. Anal Biochem 387(2):303–314

    Article  CAS  Google Scholar 

  • Hernando-Herraez I, Garcia-Perez R, Sharp AJ et al (2015) DNA methylation: insights into human evolution. PLoS Genet 11:e1005661

    Article  Google Scholar 

  • Heyn H, Moran S, Hernando-Herraez I et al (2013) DNA methylation contributes to natural human variation. Genome Res 23:1363–1372

    Article  CAS  Google Scholar 

  • Horvath S (2013) DNA methylation age of human tissues and cell types. Genome Biol 14:R115

    Article  Google Scholar 

  • Kaminsky ZA (2009) DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet 41:240–245

    Article  CAS  Google Scholar 

  • Kayser M, de Knijff P (2011) Improving human forensics through advances in genetics, genomics and molecular biology. Nat Rev Genet 12:179–192

    Google Scholar 

  • Koops BJ, Schellekens M (2008) Forensic DNA phenotyping: regulatory issues. C Sci Tech Law Rev 9:158

    Google Scholar 

  • Kwabi-Addo B, Wang S, Chung W et al (2010) Identification of differentially methylated genes in normal prostate tissues from African American and Caucasian men. Clin Cancer Res 16:3539–3547

    Article  CAS  Google Scholar 

  • Lattal KM, Abel T (2001) Different requirements for protein synthesis in acquisition and extinction of spatial preferences and context-evoked fear. J Neurosci 21:5773–5780

    Article  CAS  Google Scholar 

  • Lee HY, Park MJ, Choi A et al (2012) Potential forensic application of DNA methylation profile to body fluid identification. Int J Legal Med 126:55–62

    Article  Google Scholar 

  • Lee HY, Jung SE, Oh YN et al (2015) Epigenetic age signatures in the forensically relevant body fluid of semen: a preliminary study. Forensic Sci Int Genet 19:28–34

    Article  CAS  Google Scholar 

  • Lester BM, Tronick E, Nestler E et al (2011) Behavioral epigenetics. Ann N Y Acad Sci 1226:14–33

    Article  Google Scholar 

  • Li C, Zhao S, Zhang N et al (2013a) Differences of DNA methylation profiles between monozygotic twins’ blood samples. Mol Biol Rep 40(9):5275–5280

    Google Scholar 

  • Li X, Wei W, Ratnu VS et al (2013b) On the potential role of active DNA demethylation in establishing epigenetic states associated with neural plasticity and memory. Neurobiol Learn Mem 105:125–132

    Google Scholar 

  • Lindbo JA, Dougherty WG (2005) Plant pathology and RNAi: a brief history. Annu Rev Phytopathol 43:191–204

    Article  CAS  Google Scholar 

  • Madi T, Balamurugan K, Bombardi R et al (2012) The determination of tissue-specific DNA methylation patterns in forensic biofluids using bisulfite modification and pyrosequencing. Electrophoresis 33(12):1736–1745

    Article  CAS  Google Scholar 

  • Maze I, Covinton HE, Dietz DM et al (2010) Essential roles of the histome methyltransferase G9a in cocaine-induced plasticity. Science 327:213–216

    Article  CAS  Google Scholar 

  • Meaney MJ, Ferguson-Smith AC (2010) Epigenetic regulation of the neural transcriptome: the meaning of the marks. Nat Neurosci 11:1313–1318

    Article  Google Scholar 

  • Miller CA, Sweatt JD (2007) Covalent modification of DNA regulates memory formation. Neuron 53:857–859

    Article  CAS  Google Scholar 

  • Nielsen DA, Hamon S, Yuferov V et al (2010) Ethnic diversity of DNA methylation in the OPRM1 promoter region in lymphocytes of heroin addicts. Hum Genet 127:639–649

    Article  CAS  Google Scholar 

  • Ollikainen M, Smith KR, Joo EJ et al (2010) DNA methylation analysis of multiple tissues from new born twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome. Hum Mol Genet 19:4176–4188

    Article  CAS  Google Scholar 

  • Park JL, Kwon OH, Kim JH et al (2014) Identification of body fluid-specific DNA methylation markers for use in forensic science. Forensic Sci Int Genet 13:147–153

    Article  CAS  Google Scholar 

  • Peters TJ, Buckley MJ, Statham AL et al (2015) De novo identification of differentially methylated regions in the human genome. Epigenetics Chromatin 8:6

    PubMed  PubMed Central  Google Scholar 

  • Pirazzini C, Giuliani C, Bacalini MG et al (2012) Space/population and time/age in DNA methylation variability in humans: a study on IGF2/H19 locus in different Italian populations and in mono-and di-zygotic twins of different age. Aging 4(7):509–520

    Article  CAS  Google Scholar 

  • Rakyan VK, Down TA, Balding DJ et al (2011) Epigenome-wide association studies for common human diseases. Nat Rev Genet 12:529–541

    Article  CAS  Google Scholar 

  • Sijen T (2015) Molecular approaches for forensic cell type identification: on mRNA, miRNA, DNA methylation and microbial markers. Forensic Sci Int Genet 18:21–32

    Article  CAS  Google Scholar 

  • Terry MB, Ferris JS, Pilsner R et al (2008) Genomic DNA methylation among women in a multiethnic New York City birth cohort. Cancer Epidemiol Biomark Prev 17:2306–2310

    Article  CAS  Google Scholar 

  • Thevissen PW, Kaur J, Willems G (2012) Human age estimation combining third molar and skeletal development. Int J Legal Med 126:285–292

    Article  CAS  Google Scholar 

  • Van den Berge M, Carracedo A, Gomes I et al (2014) A collaborative European exercise on mRNA-based body fluid/skin typing and interpretation of DNA and RNA results. Forensic Sci Int Genet 10:40–48

    Article  Google Scholar 

  • Vidal-Bralo L, Lopez-Golan Y, Gonzalez A (2016) Simplified assay for epigenetic age estimation in whole blood of adults. Front Genet 7:126

    Article  Google Scholar 

  • Wang S, Dorsey TH, Terunuma A et al (2012) Relationship between tumor DNA methylation status and patient characteristics in African-American and European-American women with breast cancer. PLoS One 7(5):e37928

    Article  CAS  Google Scholar 

  • Wielscher M, Vierlinger K, Kegler U et al (2015) Diagnostic performance of plasma DNA methylation profiles in lung cancer, pulmonary fibrosis and COPD. EBioMedicine 2(8):929–936

    Article  Google Scholar 

  • Wittenberger T, Sleigh S, Reisel D et al (2014) DNA methylation markers for early detection of women’s cancer: promise and challenges. Epigenomics 6(3):311–327

    Article  CAS  Google Scholar 

  • Xu C, Qu H, Wang G et al (2015a) A novel strategy for forensic age prediction by DNA methylation and support vector regression model. Sci Rep 5:17788

    Article  CAS  Google Scholar 

  • Xu J, Fu G, Yan L et al (2015b) LINE-1 DNA methylation: a potential forensic marker for discriminating monozygotic twins. Forensic Sci Int Genet 19:136–145

    Article  CAS  Google Scholar 

  • Yong WS, Hsu FM, Chen PY (2016) Profiling genome-wide DNA methylation. Epigenetics Chromatin 9:26

    Article  Google Scholar 

  • Yuan T, Jiao Y, de Jong S et al (2015) An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet 11(2):e1004996

    Article  Google Scholar 

  • Zbieć-Piekarska R, Spólnicka M, Kupiec T et al (2015) Examination of DNA methylation status of the ELOVL2 marker may be useful for human age prediction in forensic science. Forensic Sci Int Genet 14:161–167

    Article  Google Scholar 

  • Ziller MJ, Gu H, Müller F et al (2013) Charting a dynamic DNA methylation landscape of the human genome. Nature 500(7463):477–481

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. School of Life Sciences, University of KwaZulu-Natal,Westville Campus, Durban, KwaZulu Natal, South Africa

    Meenu Ghai, Dyfed Lloyd Evans & Shailesh Joshi

Authors
  1. Meenu Ghai
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  2. Dyfed Lloyd Evans
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  3. Shailesh Joshi
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Correspondence to Meenu Ghai .

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Editors and Affiliations

  1. School of Life Sciences, University of Westminster, London, UK

    Vinood B. Patel

  2. Diabetes and Nutritional Sciences Research Division, Faculty of Life Sciences and Medicine, King’s College London, London, UK

    Victor R. Preedy

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Ghai, M., Evans, D.L., Joshi, S. (2019). Traces of Life’s Experiences: Epigenetics (DNA methylation) in Forensics. In: Patel, V., Preedy, V. (eds) Handbook of Nutrition, Diet, and Epigenetics. Springer, Cham. https://doi.org/10.1007/978-3-319-55530-0_14

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  • DOI: https://doi.org/10.1007/978-3-319-55530-0_14

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