Outline

1. Outline • Nucleosome distribution • Chromatin modification patterns • Mechanisms of chromatin modifications • Biological roles

2. Chromatin modifications

3. Profiling chromatin marks in the genome crosslink sonicate • ChIP-chip or ChIP-seq analysis is a general approach for mapping chromatin modifications in the genome • It is critical to use specific antibodies • Typically a lot of cells are needed (10^6) Chromatin IP input

4. Profiling chromatin marks in the genome • ChIP-chip or ChIP-seq analysis is a general approach for mapping chromatin modifications in the genome • It is critical to use specific antibodies • Typically a lot of cells are needed (10^6) Park PJ. Nature Reviews Genetics 10, 669-680

5. Barski et al., Cell 2007 vol. 129 (4) pp. 823-837

6. Producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. • Mapping DNA methylation, histone modifications, chromatin accessibility and RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. • Rapid release of raw sequence data, profiles of epigenomic features and higher-level integrated maps. The consortium homepage: http://epigenomebrowser.org All protocols in use can be found here, as well as information about quality metrics, news, publications, general program information, and links to other associated websites.

7. Hawkins et al., Cell Stem Cell 2010

8. Characteristic patterns of chromatin modification exist at promoters and enhancers • Enhancers are marked by H3K4me1 but NOT H3K4me3 • Promoters are marked by H3K4me3 and a depletion of H3K4me1

9. Chromatin modifications demarcate functional elements in the genome Zhou, Goren and Bernstein, Nature Rev Genetics, 2011

10. Outline • Nucleosome distribution • Chromatin modification patterns • Mechanisms of chromatin modifications • Biological roles

11. Histone acetylation reaction

12. HAT Characteristics

13. HDAC Complexes De Ruijter, et al. Biochem J. (2002)

14. Histone Methylation (lysine) • Both activation and repression • More stable • HKMT • HKDM

15. Two models of histone modifications’ roles • Histone modifications could directly alter chromatin folding. • Modified histone residues could alter the ability of histones to recruit non-histone preotinrs to chromatin, which in turn alter the abiligy of the transcriptional machinery to recognize the template.

16. Bromodomain recognizes K-ac

17. Bromodomain and lysine acetylation

18. Chromodomain and lysine methylation

19. Positional Effect Variegation in Fly Allis et al., Epigenetics, CSHL Press

20. Euchromatin and Heterochromatin Allis et al., Epigenetics, CSHL Press

21. Screening for modifiers of PEV Allis et al., Epigenetics, CSHL Press

22. Allis et al., Epigenetics, CSHL Press

25. H3K27me3 and Polycomb Complexes

26. Model for PcG silencing in cellular memory

27. Methylation of Histone H3K4 Rothenburg et al., Molecular Cell 2006

29. Histone Demethylases

30. Outline • Nucleosome distribution • Chromatin modification patterns • Mechanisms of chromatin modifications • Biological roles

31. Two different views on the propagation of cellular memory Bonasio et al. Science 2010, 330 pp. 612-6

32. Transmission of epigenetic states