Epigenetics: Introduction and Definition and the mechanism

Introduction and Definition, Factor affecting epigenetics and Inheritance, Mechanism, Epigenetic phenomenon
Cancer and epigenetics, Diagnosis , Therapies targeting epigenetic modification, Future

1. EPIGENETICS

2. OUTLINES Introduction and Definition Factor affecting epigenetics and Inheritance Mechanism Epigenetic phenomenon Cancer and epigenetics Diagnosis Therapies targeting epigenetic modification Future

3. Introduction Genetics explains phenotypic trait in organisms through presence or absence of specific nucleotide sequence of DNA. However, that does not adequately explain the expression or lack of expression of all genes. That indicates, there are other control mechanism; such as DNA methylation and chromatin modification

4. Definition C.H. Waddington coined the term epigenetics to mean above or in addition to genetics to explain differentiation Epigenetics refers to the study of changes in the regulation of gene activity and expression that are not dependent on gene DNA sequence. While epigenetics often refers to the study of single genes or sets of genes, epigenomics refers to more global analyses of epigenetic changes across the entire genome

5. Disruption of such control mechanism is associated with a variety of disease With behavioral/neurological manifestation Disorder of tissue growth Endocrine disorder Neoplasia

6. Inheritance parent’s experiences are passed on to offspring through epigenetic tags When the zygote is formed many epigenetic tags are removed from the chromosomes of the parents, but some remain

7. Identical twins from same zygote same genetic information (including epigenetic tags) While infants similar environments, so little variation in epigenome

8. Difference in the twins’ epigenomes makes them become different when they are older One can develop a disease while the other is fine

9. Methylation of Agouti Genes in Mice

10. Environment can Influence Epigenetic Changes Emma Whitelaw, Henry Stewart Talks

11. Factors during pregnancy affecting the transmission of epigenome nutrition of mother Stress, social interactions, physical activity as Stress hormones can travel from the mother to a fetus exposure to toxins

12. GRANDMOTHER’S CURSE!!!!! Some of the effects of smoking may be passed from grandmother to grandchild

13. Epigenetics Mechanisms Gene Expression RNA Interference Histone Modifications DNA Methylation

14. Epigenetic alteration are outside the primary sequence, but nonetheless affect the ability of gene to be expressed. DNA in most cells packaged with histone to form nucleosome in ‘beads on a string’ structure. Chromatin regulation involves high-order conformational changes Relaxation or tightening of this thread of DNA- histone complex

15. Further regulation is by assembling promoter-enhancer complexes via long-range DNA looping Can be blocked by specific DNA-sequence called insulator The core histones are subject to diverse post-translational modifications, including methylation and acetylation That project from tightly structured nucleosome core

16. DNA methylation

17. Histone Methylated DNA Effect of methylation Methylation turns off genes. Acetylation turn genes on.

18. 5-Methyl Cytosine is Found in Heterochromatic Regions

19. Natural Roles of DNA Methylation in Mammalian System Imprinting X chromosome inactivation Heterochromatin maintenance Developmental controls Tissue specific expression controls

20. DNA Methylation and Other Human Diseases -- Imprinting Disorder: Beckwith- Wiedemann syndrom (BWS) Prader-Willi syndrome (PWS) Transient neonatal diabetes mellitus (TNDM) -- Repeat-instability diseases Fragile X syndrome (FRAXA) Facioscapulohumeral muscular dystroph -- Defects of the methylation machinery Systemic lupus erythemtosus (SLE) Immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome

21. Histone Modifications

22. Histone modification the histone code Acetylation Methylation Phosphorylation Ubiquitylation sumoylation Enzymes catalyzing Histone acetyltransferase Histone deacetylase Histone methyltransferase Histone kina se

23. Histone Modification Status Correlates with Transcriptional Activity Gene activation correlated with H3-K9 acetylation Gene silencing associated with H3-K9 methylation

24. Role of histone modification DNA transcription DNA repair DNA replication

25. Histone Modifications and Human Diseases Coffin-Lowry syndrome is a rare genetic disorder characterized by mental retardation and abnormalities of the head and facial and other areas. It is caused by mutations in the RSK2 gene (histone phosphorylation) and is inherited as an X-linked dominant genetic trait. Males are usually more severely affected than females. Rubinstein-Taybi syndrome is characterized by short stature, moderate to severe intellectual disability, distinctive facial features, and broad thumbs and first toes. It is caused by mutations in CREB-binding protein (histone acetylation)

26. RNA interference

27. siRNA Mediated Heterochromatin Maintenance

28. X-inactivation One X-chromosome in female cells is condensed and located on nuclear periphery Complete silencing of one entire chromosome is certainly one of the most dramatic epigenetic phenomenon Key-transcript, X-inactivation specific transport lack protein-coding function

29. Production of Xist rapidly attract histone -modifying enzymes, followed in turn by DNA- methylation Inactive x-chromosome is evidently ‘locked in’ by chromatin modification- Methylation of Histone H3 at lysine K27 Hypoacetylation of histone at H3 ande H4 Dense CpG methylation of CpG islands

30. Genomic imprinting Most autosomal genes in mammalian have biallelic expression But a small number of genes are expressed from only one parental allele – Imprinting –become essential for viability Maternally derived genes are growth-limiting Paternally derived genes are growth-enhancing

31. Androgenetic and gynogenetic tumor Benign overian teratoma ( bimaternal origin) Hydatidiform mole ( biparenatal origin) Usually benign Diagnosis: histopathology + immunostaining of protein product of imprinted gene Neoplastic trophoblast of complete hydatidiform mole fails to express imprinted gene (CDKN1C and PHLDA2)- those normally imprinted from maternal allele

32. Prader-willi and Angelman syndrome Chromosomal band 15q11-q13 is a megabase scale chromosomal domain including multiple imprinted gene One portion of gene is maternally expressed/paternally silenced Adjacent portion oppositely imprinted Deletion of paternal homologue – PWS Deletion of maternal homologue - AS

33. Whether these diseases are due to large deletion, microdeletion , epimutation majority can be diagnosed by simple Southern blot or PCR-based assays for DNA mutation Gain of methylation in PWS Loss of mutation kin AS

34. Cancer epigenetics A common paradigm of cancer epigenetics is hypermethylation of CpG island of tumor suppressor gene promoter Hypermethylated promoter DNA is associated with virtually every type of human tumor With each type of tumor having own signature of methylated genes

35. Cancer Methylated genes Prostate GSTP1 Renal VHL Colon and endometrial MLH1 (mismatch repair gene) Esophageal APC

36. Global hypomethylation : overall in 5-methylcytosine content in the genome Found in premalignant and early stages of some neoplasm Important in tumor progression Gene-specific hypomethylation : Often affect promoter region of proto-oncogene and oncogene which are normally highly methylated

37. DNA Methylation and Cancer

38. Technologies for Studying Epigenetics/Epigenomics DNA Methylation Irizarry et. Al. (2008) Genome Research 18(5):780 Microarray or deep sequencing

39. Bisulfite Sequencing

40. 5’ 3’ Expression array Exon array Splicing array Promoter array Tiling array exon intron Global Interrogation of DNA Methylation using Microarrays promoter

41. Earliest method, still the most direct and least subject to artifact is southern blotting of genomic DNA with methylation -sensitive restriction enzyme. Restriction enzymes ( e.g. Hpa ІІ , Sma І , Not І ) with CpG as part of their recognition sequence do not cut that sequence when the C is methylated

42. Technologies for Interrogating Epigenetics/Epigenomics http://www.nature.com/jid/journal/v125/n2/extref/5603467x1.jpg ChIP-chip Antibody specific to one type of histone modification Histone Modifications ChIP-seq Deep sequencing

43. Demethylation in cancer therapy

44. HDAC inhibitors

45. Interchromosome regulation of genes

46. Scaffold protein SATB1 More higher structure than chromatin Play important role in T-cell development