1. Histone Methylation Marks : Permanent or Reversible?

2. Epigenetics Background Study of heritable changes in gene expression that are not due to changes in DNA sequence DNA methylation Histone Code Chromatin Remodeling

3. Histone Code Implications: 1. Combination of differentially modified neucleomes higher order chromatin 2. Different modifications interact with each other, either synergistic or antagonistic 10 AUGUST 2001 VOL 293 SCIENCE

4. Methylation Sites and Chemical Structures Cell, Vol. 109, 801–806, June 28, 2002

5. Difference between Histone Methylation and Acetylation MethylationAcetylation Modifica tion Site Lysine and Arginine Lysine StabilityGenerally reversible Generally stable FunctionTranscriptional Activation OR Repression Generally Transcriptional Activation

6. Methylation Marks-Dynamic or Static? Considerably lower turnover than phosphorylation and acetylation The same turnover as Histone No HDMase identified then Stable “Methylation Marks”

7. Inheritable Methylation Marks Cell 125, April 21, 2006

8. Biological Role of Methylation Marks Oncogenesis(Activating Oncogene Transcription) H3K4me2 Long-term silencing Hox gene: H3K9me2, H3k27me3 Inactivating X chromosome in female mammals: H3k27me3, H3K9me2, H4K20me1 Maintaining ES cell pluripotency and plasticity: H3k27me3

9. Mechanism of Gene Silencing Mediated by Histone Methylation

10. Events Against the “Stable” Nature of Histone Methylation Cyclin E Promoter Yeast Promoter Active Inactive G1 S Inactivated Activated H3K9 MethylationH3K9 Demethylation? H3K4 TrimethylationH3K4 Dimethylation

11. How can Methylation Marks be Removed? Cell, Vol. 109, 801–806, June 28, 2002

12. Groundbreaking Experiment: Identification of the First Histone Demethylase First enzyme responsible for histone lysine demethylation LSD1 DiMeH3K4 Cell, Vol. 119, 941–953, December 29, 2004

13. Hints: KIAA0601(LSD1) involved in various corepressor complex SPR-5 (C. elegans homolog) involved in transcriptional repression Target: try to find out what KIAA0601 do and how it works

14. LSD-1 is Evolutionarily Conserved

15. LSD-1 Is a Transcriptional Repressor

16. Demethylation of diMeK4H3 Peptides by LSD1

18. Specific Demethylation at K4 of Histone H3 by LSD1 but Not LSD1C

19. LSD1 Converts diMeK4H3 Peptides to Peptides with Molecular Weight Corresponding to Unmodified H3

20. LSD1 Regulation of Endogenous Target Gene Transcription and H3-K4 Methylation In Vivo

21. Conclusion LSD1 represses Gene Transcription via Directly Demethylating Histone DimeH3K4

22. Other Methyl Marks found to be Demethylated JMJD3: Demethylate TriMeH3K27 Mouse Neural Stem Cells: RA JMJD3 Differentiation(Nature,Vol 450(15) November 2007) RAW264.7 Macrophage: LPS NF-kappa B JMJD3 macrophage plasticity (Cell 130, 1083–1094, September 21, 2007)

23. JMJD3,UTX Cell 125, April 21, 2006 Currently Identified Histone Demethylase

24. Perspective Characterization of More Demethylases and Their Biological Roles Reveal More Key Regulatory Processes Dependent on Reversal of “Stable Methylation Marks”