1. Epigenetics: from Inheritance to Cancer Maxwell Lee National Cancer Institute Center for Cancer Research Laboratory of Population Genetics April 21, 2011

2. Definitions of Epigenetic and Epigenetics Epigenetic is related to epigenesis---The theory that an individual is developed by successive differentiation of an egg rather than by a simple enlarging of a preformed entity. Epigenetics = epigenesis + genetics---developmental processes that initiated by genotype but don’t involve changes in genetic materials. By Conrad Waddington

3. Dualism of Genetic and Epigenetic Inheritance systems Genetics---Genetic inheritance vs. mutation, which operate on individuals to change DNA sequences in the spaces of evolution, population, and pedigree. Epigenetics---Cellular memory vs. plasticity, which operate on cells to change epigenetic states in the spaces of development, differentiation, and physiology.

4. Definitions of Epigenetic and Epigenetics Epigenetic is related to epigenesis---the theory that an individual is developed by successive differentiation of an egg rather than by a simple enlarging of a preformed entity. Epigenetics = epigenesis + genetics---developmental processes that initiated by genotype but don’t involve changes in genetic materials. By Conrad Waddington Epigenetics---the study of mitotically and/or meiotically heritable changes in gene function that can not be explained by changes in DNA sequences. Biochemical basis of epigenetics---DNA methylation and chromatin structure/modifications. Function of epigenetics---gene expression regulation. Modern Definition of Epigenetics

5. Chromatin and DNA Methylation

6. 5-methylcytosine

7. DNA Methylation and Methyl Transferase

8. Effects of DNA Methylation on Chromatin and Transcription

9. Interaction between DNA Methylation and Chromatin

10. Examples of Epigenetic Phenomena

11. Multiple Layers of Epigenetic Information Epigenetic information at the organism level Epigenetic information at the cellular level Epigenetic information at the allelic level

12. Genomic Imprinting Gynogenetic lethal Androgenetic lethal normal

13. Igf2 Phenotype is Paternally Transmitted

14. Beckwith-Wiedemann syndrome (BWS) The cardinal features of this disorder are exomphalos, macroglossia, and gigantism in the neonate. Patients have enlarged tongue, together with omphalocele or other umbilical abnormalities. Visceromegaly, adrenocortical cytomegaly, and dysplasia of the renal medulla are conspicuous features. Adrenal carcinoma, nephroblastoma, hepatoblastoma, and rhabdomyosarcoma occur with increased frequency. BWS is caused by mutation in P57KIP2 and LOI of LIT1 and IGF2.

15. Beckwith-Wiedemann Syndrome (BWS) Adrenal carcinoma, nephroblastoma, hepatoblastoma, and rhabdomyosarcoma.

16. P57KIP2 Mutation in Beckwith-Wiedemann Syndrome (BWS)

17. Loss of Imprinting (LOI) of A Regulatory RNA in BWS mat pat N*BB 6 kb 4.2 kb matpatepigenotype

18. Beckwith-Wiedemann syndrome (BWS) mat pat mat pat mat pat

19. Loss of Imprinting (LOI) in Cancer

20. Epigenetics and Allelic Variation in Chromatin 5mC5mCH3K9-Me H3-Ac Inactive Active RNA X inactivation and genomic imprinting TF Pol II Repressor Inter-individual and intra-individual variation

21. Allelic-specific Chromatin State Determined By ChIP-on-chip Method

22. Inheritance Analysis Of Allelic Histone H3 Acetylation State

23. Allelic-specific DNA Methylation Kerkel et al, 2008

24. Heritable Germline Epimutation of MSH2 in a HNPCC Family Chan et al., 2006

26. Heritable Epimutation of MSH2 in HNPCC due to Deletion of the 3’ Exons of TACSTD1 Ligtenberg et al., 2009

29. Extension to Knudson’s Two-hits Hypothesis Part 2 Epigenetic silencing

30. Epigenetic Silencing of Tumor Suppressor Genes in Human Cancer Part 2

31. How Epigenetics Affects Genetics? Part 2

32. Multistage Cancer Progression Model

33. Distribution of CpG Sites in Human Genome

34. Distribution of Methylation at CpG Sites in Human Genome

35. Methylation of Human Chromosomes

36. Common Methods Used in DNA Methylome Studies Bisulfite-treated DNA genomic DNA Sequencing Illumina MSO microarry MeDIP McrBC Hpa II enrichment

37. High-throughput DNA Methylation Profiling Using Universal Bead Arrays

38. High-throughput DNA Methylation Profiling Using Universal Bead Arrays

39. Distribution, Silencing Potential and Evolutionary Impact of Promoter DNA Methylation in the Human Genome

41. MethylScope Array (McrBC)

42. HpaII Enrichment by Ligation-mediated PCR (HELP)

43. DNA Methylation Profiling of Human Chromosomes 6, 20 and 22

45. Comparison of Sequencing-based Methods to Profile DNA Methylation