Epigenetics – a New Perspective for Imppgroving Forensic...
Transcript of Epigenetics – a New Perspective for Imppgroving Forensic...
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Epigenetics – a New Perspective for Improving Forensic Sciencep g
Hwan Young Lee, Ph.D.Department of Forensic MedicineYonsei University College of Medicine
Forensic cases -- matching suspect with evidence
Paternity testing -- identifying father
Current Forensic DNA Typing
Paternity testing identifying father
Involves generation of DNA profiles usually with the same genetic
markers and then MATCHING TO REFERENCE SAMPLE
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Challenges in Crime Scene Investigation
Technical challenges in forensic STR profiling
Degraded DNA Degraded DNA
Low amount of DNA
Increasing discrimination power
Familiar searching….
Important challenges remain for the use of genetic and Important challenges remain for the use of genetic and
epigenetic approaches in forensic investigations
Kayser M and de Kniff P, Nat Rev Genet (2011)
Future of Crime Scene Investigation
The ability to infer biogeographic ancestry and external
visible characteristics from DNA
Eye (IrisPlex), hair and skin color
Freckles
Stature
Hair morphology
Male baldness, etc.
http://meglikestodraw.tumblr.com/Kayser M and de Kniff P, Nat Rev Genet (2011)
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Body fluid identification can provide information linking
sample donors with actual criminal acts
Future of Crime Scene Investigation
Detailed reconstruction of crime events by determining
the time of sample donation and sample age
Kayser M and de Kniff P, Nat Rev Genet (2011)
Body fluids founds on the bedSex offender’s trial
Genetics and Epigenetics
Epi (on top of or in addition to) + Genetics
Epigenetics is the study of heritable changes in gene
expression or cellular phenotype caused by mechanisms
other than changes in the underlying DNA sequence
Genome – Epigenome, Genetic code – Epigenetic code
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What is a Epigenome?
DNA methylation
Histone modification Histone modification
MicroRNA
http://learn.genetics.utah.edu/content/epigenetics/
Methyl tag Acetyl tag
DNA Packaging
Felsenfeld G and Groudine M, Nature (2003)
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Gene Control by the Epigenome
http://learn.genetics.utah.edu/content/epigenetics/
Gene Control by the Epigenome
Epigenome is flexible and epigenetic tags react signals, e.g.,
diet, stress, etc
http://learn.genetics.utah.edu/content/epigenetics/
Methyl tag
Acetyl tag
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Epigenetic Tags and Cellular Memory
A cell’s epigenetic profile – a collection of tags that tell
genes whether to be on or off – is the sum of the signals itg g
has received during its lifetime
Epigenetic profiles are specific to tissue, age and
environmental factors
http://learn.genetics.utah.edu/content/epigenetics/
DNA Methylation
DNA methylation is the addition of a methyl group to the
DNA base cytosine followed by a guanine (5' CG 3')DNA base cytosine followed by a guanine (5 CG 3 )
Cytosine 5-Methyl Cytosine
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tDMRs and Body Fluid Identification
Chromosome pieces called tDMRs (tissue-specific
differentially methylated regions) show different DNAdifferentially methylated regions) show different DNA
methylation profiles according to the type of cell or tissue.
Tissue UCSC location (Mar. 2006) CGI Gene Function References
Testis chr14:58182690–58182995 cpgi50 DACT1 Dapper 1 isoform 2 Genomics. 89:326
Testis chr6:41881884–41882111 cpgi46 USP49 Ubiquitin carboxyl-terminal hydrolase 49 Genomics. 89:326
Table. Genomic information for candidate tDMRs for body fluid identification
Blood chr7:27135995–27136879 cpgi87 HOX44 Homeobox protein Hox-A4 PLoS Biol. 6:e22
Blood chr5:176758438–176760564 cpgi82 PFN3 Profilin-3 PLoS Biol. 6:e22
Blood chr21:46905647–46905874 cpgi55 PRMT2 Protein arginine N-methyltransferase 2 PLoS Biol. 6:e22
Lee HY et al. Int J Legal Med (2012)
Analysis of DNA Methylation
Met Met
Sodium bisulfite conversion
CpG
CpG
CpG
UpG
CpG
TpG
Sodium bisulfite PCR Sequencing
SBE
MSP
MSRE-PCR
Methylation-sensitive restriction enzyme
PCR product
No PCR product
PCRCpG
CpG
CpG
CpG
Met Met
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DNA methylation profiles for the DACT1, USP49,HOXA4, PRMT2 and PFN3 tDMRs in pooled DNA
l f bl d li l bl d d
Differential DNA Methylation
: DACT1 : USP49
samples from blood, saliva, semen, menstrual blood andvaginal fluid
Lee HY et al. Int J Legal Med (2012)
DNA methylation profiles for the DACT1, USP49,HOXA4, PRMT2 and PFN3 tDMRs in pooled DNA
l f bl d li l bl d d
Differential DNA Methylation
: DACT1 : USP49: HOXA4 : PRMT2
samples from blood, saliva, semen, menstrual blood andvaginal fluid
Lee HY et al. Int J Legal Med (2012)
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DNA methylation profiles for the DACT1, USP49,HOXA4, PRMT2 and PFN3 tDMRs in pooled DNA
l f bl d li l bl d d
Differential DNA Methylation
: DACT1 : USP49: HOXA4 : PRMT2: PFN3
samples from blood, saliva, semen, menstrual blood andvaginal fluid
Lee HY et al. Int J Legal Med (2012)
DNA Methylation and Aging
The DACT1, USP49 and PRMT2 tDMRs in pooled DNAsamples from blood, saliva and semen obtained from 20
( 30 ) d 15 ld ( 50 )young (< 30 y) and 15 old (> 50 y) men
: DACT1 : USP49
: PRMT2
An JH et al. Int J Legal Med in press
: PRMT2
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Methylation-Specific Multiplex Assays
MSRE-PCR Methylation-SNaPshot
Blood
Saliva
Menstrual blood
An JH et al. Int J Legal Med in press
Vaginal fluid
Semen
DNA Methylation and Age Estimation
The methylation of three sites—in the promoters of the
EDARADD NPTX2 and TOM1L1 genes—is linear withEDARADD, NPTX2 and TOM1L1 genes is linear with
age over a range of five decades in saliva.
Percentage methylation versus age for three markers, (a) EDARADD, (b) NPTX2 and (c) TOM1L1
Bocklandt et al. PLoS One (2011)
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Age Estimation Using Body Fluids
TOM1L1SPAG7
ALDH1A1 WISP2 EDARADD
20sTOM1L1
SPAG7ALDH1A1 WISP2 EDARADD
20s
DNA Methylation in Saliva DNA Methylation in Semen
20s
30s
50s
50s
20s
50s
50s
DNA Methylation in Skin EpidermisTOM1L1
SPAG7ALDH1A1 WISP2 EDARADD
20s
30s
60s
Discrimination Between Identical Twins
Identical twins exhibit differences in DNA methylationprofile
Fraga MF et al. Proc Natl Acad Sci U S A (2005), Zhao SM et al. Fa Yi Xue Za Zhi (2011)
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Detection of Fabricated DNA Evidence
Natural and artificial DNA are distinguishable based on
methylation analysis of a set of genomic loci: in artificialy y g
DNA, all loci are unmethylated
Bisulfite sequencing
Natural
Frumkin D et al. Forensic Sci Int Genet (2010), New York Times- Aug 17, 2009
Artificial
Current View of Human Epigenome
DNA methylation
Histone modification Histone modification
Small RNAs
Microarray
Next Generation Sequencing…
Schones DE and Zhao K, Nat Rev Genet (2008)
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The Future of Forensic DNA Typing
Genetics, Genomics, Epigenetics, Epigenomics, Epitranscriptomics…
Thank you for your attention!
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