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Decoding epigenome with integrative “omics” data analysis

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

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Decoding epigenome with integrative “omics” data analysis

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  1. Decoding epigenome with integrative “omics” data analysis Hehuang “David” Xie Sept, 2014

  2. 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

  3. Epigenetics Epigeneticsis the study of heritable changes in gene activity that are NOTcaused by changes in the DNA sequence. http://en.wikipedia.org/wiki/

  4. Epigenetic codes • DNA methylation • Histone modifications https://www.caymanchem.com http://cnx.org/content/m44536/latest/

  5. Methylation & iPSC Reprogramming http://ips-cell.net/e/ips/index.html

  6. 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

  7. : methylated mCG Methylation Level vs Methylation Pattern mCG mCG CG CG Sequence read: Methylation level = 50% : unmethylated CG Sequence read: Pattern 4: Pattern 1: Pattern 3: Pattern 5: Pattern 2:

  8. Epigenetic Heterogeneity Locus 2 Locus 1 Locus 4 Locus 3 M P M M P A) Homogenous B) Bipolar C) Heterogeneous P M P a) Asymmetric DNA methylation c) Cell-subset specific methylation (CSM) b) Allele specific methylation (ASM) 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.

  9. Genome-wide Hairpin Bisulfite Sequencing mCG mCG mCG CG GCm GCm GC GCm Sonication or enzyme digestion mCG: methylated CpG CG: unmethylated CpG : biotinylated hairpin adaptor : Illumina adaptor Adaptor Ligation Pull down with dynabeads Bisulfite PCR mCG mCG mCG CG GCm GCm GC GCm mCG mCG mCG TG TG mCG Zhao et al. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation.Genome Research 2014

  10. SSM, CSM and Hairpin Bisulfite Sequencing M M M M M P P P P P M M M P P P Completely Unmethylated Asymmetric DNA Methylation Cell-subset Specific Methylation Completely Methylated

  11. SSM, CSM and Histone Modifications Active enhancer Promoter Enhancer Gene body or Intergenic regions Completely Unmethylated Completely Methylated Asymmetric DNA Methylation Cell-subset Specific Methylation Strand specific methylated CpG sites enriched in gene body with H3K36me3 marks Cell specific methylated CpG sites enriched in active enhancers with H3K27ac and H3K4me1 marks

  12. SSM, CSM and TF Bindings Completely Unmethylated Completely Methylated Asymmetric DNA Methylation Cell-subset Specific Methylation Strand specific methylated CpG sites depleted from TF binding sites Cell specific methylated CpG sites enriched in a number of TF binding sites

  13. 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

  14. Epigenetic dynamics of developing brain Genomic DNA methylation pattern from a mixed cell population Cell 1 A B C D Cell 2 A B C D Cell 3 A B C D Cell 4 A B C D Cell 5 A B C D Cell 6 A B C D . . . Cell n A B C D

  15. Ongoing Research Enhancer maps Xie et al, Cell 2012 Nord et al, Cell 2013 Zhu et al, Cell 2013 Anderssonet al, Nature 2014 TF binding maps Encode Project, Nature 2012 Brain Methylome Science 2013 Hairpin Methylome Genome Research 2014 Transcriptome ALLEN Brain Altas, Cell 2013 Mazi et al, MSB 2013 • Genetic mutations • Khurana et al, Science 2013 • Human Gene Mutation Database • GWAS catalogue

  16. Epigenetic dynamics of developing brain CSM frequencies increase dramatically at early stages of brain development.

  17. GO enrichment for CSM associated genes The CSM associated genes are enriched for function related to brain development.

  18. CSM and Histone Modifications

  19. TF binding enrichment in CSM regions

  20. Disease-associated genetic variations in CSM regions Color Key and Histogram

  21. 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 dramaticincrease 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

  22. Acknowledgements • Collaborators • Dr. VeenaRajaram (UTSW) • Dr. Xiaowei Wu (VT) • Dr. Liqing Zhang (VT) • Dr. Jianjun Chen (UC) • Dr. Chuan He (UC, HHMI) • Dr. HenkStunnenberg • (Netherlands, Radboud University) • Dr. Wolf Reik (UK, Cambridge) • Dr. Haruhiko Koseki (Riken Institute) • Dr. Xuemei Lu (China, BIG) • Xie’s lab • Dr. Lei Zhao • Dr. Ming-an Sun • Dr. Zhenqing “James” Xie • Dr. Ni Li • Zhixiong “Kevin” Sun • KarthikrajaVelmurugan • David Keimig • Jessica Lim • Sarah Sam

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