1. Lecture outline 1.Class organization 2.Introduction to Epigenetics

2. Lecture outline 1.Class organization a.Target audience b. Organization: lecture, research lecture, student presentations

4. Lecture outline 1.Class organization a.Target audience b. Organization: lecture, research lecture, student presentations c. What is expected: attendance, participation, questions for the student papers 2 exams (recitations before them) student presentations (grad and CAMB enrolled: final proposal)

5. Student presentations 1. TWO volunteers for next week (September 13 th ): chromatin assembly 2. For all other slots: everyone needs to present, choose a date or topic and e-mail me as soon as possible IMPORTANT: if you decide to drop the class and have chosen a presentation date already please let me know 3. If >19 students then we double up on papers one students presents the background of the field plus the first half of the paper the second student does the second half of the paper and future directions

6. Lecture outline 1.Class organization 2.Introduction to Epigenetics what are epigenetic phenomena where does epigenetic regulation occur

7. Epigenetic phenomena: heritable alternative states of gene activity that do not result from altered nucleotide sequence

8. Examples of Epigenetic Phenomena Monozygotic: Genomes are identical

9. Examples of Epigenetic Phenomena Monozygotic (identical) twins and disease etiology Arturas Petronis 2006 Monozygotic: Genomes are identical

10. Examples of Epigenetic Phenomena Monozygotic: Genomes are identical

11. Cloned cat: Genome is identical Yet looks different from mother Rainbow and Copycat

12. Calico cat coat color cannot be cloned!!! Not based on genetics Based on Epigenetics: Color gene is X-linked Random X-inactivation of cells in blastula all daughter cells will inherit that pattern Rainbow and Copycat

13. Genetics vs. Epigenetics +germline invariable

14. * transient (not heritable) * mitotically heritable * meiotically heritable

15. Plants: many examples of meiotically heritable or transgenerational epigenetic phenomena http://learn.genetics.utah.edu/content/epigenetics/inheritance/

16. Animals: fewer examples known

17. Kaati, G., Bygren, L.O., Pembrey, M., and Sjostrom, J. (2007). Transgenerational response to nutrition, early life circumstances and longevity. European Journal of Human Genetics 15: 784-790. http://learn.genetics.utah.edu/content/epigenetics/inheritance/ Animals: fewer examples known

18. Human transgenerational epigenetic phenomena? Time magazine 2010 Utah Epigenetics website View NOVA special “A ghost in your genes” http://en.sevenload.com/videos/tX02lnf-Nova-The-Ghost-In-Your-Genes-1-6

19. Nucleus; chromatin The material for Epigenetics

20. The conundrum Human DNA: 2 m Human nucleus r = 10 µm 10,000 x compaction Starting at the beginning

23. The solution DNA is compacted via interaction with proteins THIS IS THE TEMPLATE FOR EPIGENTIC PHENOMENA

24. Nucleosome Chromatin organizes and compacts DNA from Horn and Peterson Science, 2002 ac DNA methylation

25. Woodcock and Dimitrov, COGD, 2001 Caterino and Hayes, Nature Structural and Molecular Biology, 2007 Chromatin structures

26. Primary structure the NUCLEOSOMAL DNA

27. Beads on a string

28. Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome Roger D. Kornberg and Yahli Lorch; Cell, 1999.

29. Nucleosome: 147 bp of DNA Histone octamer = 1.7 turns

30. The nucleosome: histones plus DNA

31. HISTONES

35. Two classes of histones (canonical) Core Histones H2Aconserved H2Bconserved H3highly conserved H4very highly conserved Linker Histones H1 not conserved Small proteins, ca. 10 kD, very basic Three domains A. Histone fold B. Histone fold extension C. Extended N (and C)-termini

36. Tails are K (lysine) and R (argenine) rich Histone fold: 3 conserved alpha helices Histone fold extension and N-termini C-termini Linker histone

37. HISTONE/ DNA INTERACTIONS 1. Charge neutralization: basic residues lysine, argenine 2. Hydrophobic side chains; threonine, proline, valine, isoleucine with deoxyribose 3. Main chain amide with phosphate oxygen

38. Canonical histones and histone variants

39. Secondary structure 30 nm fiber linker histone

40. Nucleosome Chromatin organizes and compacts DNA from Horn and Peterson Science, 2002 ac DNA methylation

41. Nucleosome Chromatin restricts accessibility of the genome from Horn and Peterson Science, 2002 ac DNA methylation

42. Types of Chromatin

43. Euchromatin Transcriptionally active, less compacted Heterochromatin Less transcriptionally active, very compacted a) constitutive heterochromatin centromeres, telomeres b) facultative heterochromatin rDNA, transposons, inactive X chromosome

44. Heterochromatin (stained) http://www.biology.wustl.edu/faculty/elgin/hp2chrom.jpg www.nenno.it/publications/mnphdthesis/diss08.jpg

45. Barr Body Region * Immunofluorescent straining of the human interphase nucleus. * The white box indicates the Barr body region where the inactive X chromosome resides during interphase. Chadwick and Willard (2004) PNAS

46. Nucleosomes are obstacles to transcription Hodges et al. Science 2009

47. Transcription happens outside of condensed chromatin 2003

48. Transcription happens outside of condensed chromatin

49. DNA that contacts histones is not readily accessible

50. Nucleosome: 147 bp of DNA Histone octamer = 1.7 turns

51. Regular linker size: common in inactive chromatin Irregular linker size: common in active chromatin Linker size is variable: 10-50 bp Nucleosome position and spacing matters

52. Luger et al. Nature, 1995 Histone tails are modified, this influences accessibility of the genomic DNA

53. Latham and Dent Nat Struct Mol Biol 2007 Histone modifications matter

54. DNA methylation status is important Nature News, May 2006

55. All levels of chromatin condensation have been implicated in controlling accessibility of the genomic DNA effect on: replication, recombination, repair, and transcription

56. Nucleosome Chromatin restricts accessibility of the genome from Horn and Peterson Science, 2002 ac DNA methylation

57. Nucleosome Chromatin regulators alter accessibility of the genome from Horn and Peterson Science, 2002 ac DNA methylation

58. Mechanism exist to “open up” chromatin Chromatin remodeling complexes alter primary structure of chromatin Histone modifying enzymes alter histone tail modifications Leschziner lab, Harvard

59. Mechanism exist to “condense” chromatin Histone modifying enzymes alter histone tail modifications DNA methylases, Recruitment of chromatin binding proteins Polycomb proteins Heterochromatin Protein Francis Science 2005

60. Mechanism exist to “open up” chromatin Chromatin remodeling, histone modifications Mechanism exist to “condense” chromatin Histone modifications, DNA methylation, chromatin binding proteins Can alter gene activity without change in DNA Can alter gene activity without change in DNA

61. Regulatory roles of chromatin if yes: EPIGENETIC REGULATION if no: CHROMATIN REGULATION Is it the existing chromatin state heritable? Is it the existing chromatin state heritable?

62. Chromatin-based restriction of genome accessibility during differentiation Selective activation of genome after perception of stimulus (influence of environment/stress) Mitotic maintenance of cell identity (or loss thereof in cancer) Dosage compensation in the male versus female genome (X inactivation in mammals) Memory, Behavior, Aging Epigenetic/chromatin phenomena

63. HDAC Inhibitor treated Pelag et al., Science 2010

64. Chemotherapy plus HDAC inhibitor? Sharma et al. Cell 2010

65. Change in histone modification alters lifespan Greer et al., Nature 2010

66. Lecture outline 1.Class organization check blackboard site 2. Introduction to Epigenetics next chromatin assembly chromatin remodeling histone modifications histone variants

67. Nucleosome: DNA plus histone octamer DNA wound around the histone octamer: core DNA DNA between nucleosomes: linker DNA Glossary Chromatin: nucleosomal arrays

68. Differences in the epigenome of monozygotic twins Fraga et al. PNAS, 2005