decoding epigenome with integrative “omics” data analysis
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Decoding epigenome with integrative “omics” data analysis. Hehuang “David” Xie Sept, 2014. Presentation Outline. Introduction to Epigenetic codes Genome-wide Hairpin Bisulfite Sequencing Application on embryonic stem cell renewal and differentiation - PowerPoint PPT PresentationTRANSCRIPT
Decoding epigenome with integrative “omics” data analysis
Hehuang “David” XieSept, 2014
Presentation Outline
– Introduction to Epigenetic codes
–Genome-wide Hairpin Bisulfite Sequencing• Application on embryonic stem cell renewal and
differentiation
– Decoding brain epigenome with integrative “omics” data analysis
Epigenetics
Epigenetics is the study of heritable changes in gene activity that are NOT caused by changes in the DNA sequence.
http://en.wikipedia.org/wiki/
Epigenetic codes DNA methylation
https://www.caymanchem.com
Histone modifications
http://cnx.org/content/m44536/latest/
http://ips-cell.net/e/ips/index.html
Methylation & iPSC Reprogramming
Presentation Outline
– Introduction to Epigenetic codes
–Genome-wide Hairpin Bisulfite Sequencing• Application on embryonic stem cell renewal and
differentiation
–Decoding brain epigenome with integrative “omics” data analysis
Methylation Level vs Methylation Pattern
CGmCGmCG CGSequence read:
: methylated mCG: unmethylated CG
Sequence read:
Methylation level = 50%
Pattern 1:
Pattern 2:
Pattern 4:
Pattern 5:
Pattern 3:
Epigenetic Heterogeneity
Diverse methylation patterns reflect distinct epigenetic events. Each line represents a sequence read or a DNA strand; open circle represents unmethylated cytosine; filled circle represents methylated cytosine; “M” and “P” indicate maternal and paternal alleles.
A) Homogenous B) Bipolar C) Heterogeneous
M
P
M
P
M
P
M
P
a) Asymmetric DNA methylation
b) Allele specific methylation (ASM)
c) Cell-subset specific methylation (CSM)
Locus 1 Locus 2 Locus 3 Locus 4
mCGmCGmCG CGGCmGCGCmGCm
Sonication or enzyme digestion
Adaptor Ligation
Pull down with dynabeads
Bisulfite PCR
mCGmCGmCG CGGCmGCGCm
mCGmCG TG mCG TG mCG
mCG: methylated CpG
CG: unmethylated CpG
: biotinylated hairpin adaptor
: Illumina adaptor
GCm
Genome-wide Hairpin Bisulfite Sequencing
Zhao et al. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation. Genome Research 2014
SSM, CSM and Hairpin Bisulfite Sequencing
Cell-subset Specific Methylation
M
P
M
P
Asymmetric DNA Methylation
M
P
M
P
M
P
M
P
Completely Methylated
Completely Unmethylated
M
P
M
P
Completely Unmethylated
Completely Methylated
Asymmetric DNA Methylation
Cell-subset Specific Methylation
1) Strand specific methylated CpG sites enriched in gene body with H3K36me3 marks2) Cell specific methylated CpG sites enriched in active enhancers with H3K27ac and
H3K4me1 marks
SSM, CSM and Histone Modifications
Active enhancer
Enhancer
Gene body orIntergenic regions
Promoter
Completely Unmethylated
Completely Methylated
Asymmetric DNA Methylation
Cell-subset Specific Methylation
1) Strand specific methylated CpG sites depleted from TF binding sites2) Cell specific methylated CpG sites enriched in a number of TF binding sites
SSM, CSM and TF Bindings
Presentation Outline
– Introduction to Epigenetic codes
–Genome-wide Hairpin Bisulfite Sequencing• Application on embryonic stem cell renewal and
differentiation
–Decoding brain epigenome with integrative “omics” data analysis
Epigenetic dynamics of developing brain
Genomic DNA methylation pattern from a mixed cell population
Cell 1 A B DCCell 2 A B DCell 3 A B DCell 4 A B DCell 5 A B DCell 6 A B D
C
CC
CC
Cell n A B DC
.
.
.
Ongoing Research
Brain Methylome Science 2013
Hairpin MethylomeGenome Research 2014
Enhancer mapsXie et al, Cell 2012Nord et al, Cell 2013Zhu et al, Cell 2013Andersson et al, Nature 2014
TF binding mapsEncode Project, Nature 2012
TranscriptomeALLEN Brain Altas, Cell 2013Mazi et al, MSB 2013
Genetic mutationsKhurana et al, Science 2013Human Gene Mutation DatabaseGWAS catalogue
CSM frequencies increase dramatically at early stages of brain development.
Epigenetic dynamics of developing brain
The CSM associated genes are enriched for function related to brain development.
GO enrichment for CSM associated genes
CSM and Histone Modifications
TF binding enrichment in CSM regions
Samples Diseases\Traits
Addiction
Alzheimer's disease
Attention deficit hyperactivity and conduct disorder
Bipolar disorder and schizophrenia
Eating disorders
Helicobacter pylori serologic status
Multiple sclerosis
Parkinson's disease
Stroke
Fetal 35d 2y 5y 12y 16y 25y 53G 53N 55G 55N
Color Key and Histogram
Disease-associated genetic variations in CSM regions
Summary
• The combination of hairpin bisulfite sequencing and computational approach assist in the distinction of cell-subset specific methylation from allele-specific and asymmetric DNA methylation; • Mammalian brain development is accompanied with a dramatic increase in the number of cell-subset specific methylated loci;
• Cell-subset specific methylation is highly correlated with histone marks for active enhancers and enriched in transcription factor binding;
• Genetic variations associated with neurological disorders are enriched in brain cell-subset specific methylated regions
AcknowledgementsXie’s lab
• Dr. Lei Zhao
• Dr. Ming-an Sun
• Dr. Zhenqing “James” Xie
• Dr. Ni Li
• Zhixiong “Kevin” Sun
• Karthikraja Velmurugan
• David Keimig
• Jessica Lim
• Sarah Sam
Collaborators
• Dr. Veena Rajaram (UTSW)
• Dr. Xiaowei Wu (VT)
• Dr. Liqing Zhang (VT)
• Dr. Jianjun Chen (UC)
• Dr. Chuan He (UC, HHMI)
• Dr. Henk Stunnenberg
(Netherlands, Radboud University)
• Dr. Wolf Reik (UK, Cambridge)
• Dr. Haruhiko Koseki (Riken Institute)
• Dr. Xuemei Lu (China, BIG)