Epigenetics

1. Epigenetics 12/05/07

2. Epigenetic regulation is critical for cell differentiation

3. Gene imprinting

4. More examples of epigenetic regulation

5. Epigenetic mechanisms • DNA methylation • Histone modification • Nucleosome positions

6. DNA methylation Alberts et al. Molecular Biology of the Cell

7. Methylated genes are silenced

8. Probable mechanisms for DNA methylation induced siliencing • The DNA methylation marker directly interferes with TF binding. • The DNA methylation marker is recognized by proteins that cause chromatin structure changes.

9. DNA in the nucleus is complexed with histones to form nucleosomes 10,000 nm 11 nm 30nm 1bp (0.3nm)

10. Acetyl Ubiquityl Methyl Phosphoryl Histone modification Luger et al.Nature, (1997) Histone tails can be covalently modified in multiple ways at multiple sites Felsenfeld and Groudine, Nature, (2003)

11. How histone modfication is inherited • Histone methylation marks may be inherited by local concentration. • The exact mechanism for inheritance is unknown. • Even if histone modification is inherited is not proved.

12. TF TF TF TF Transcriptional regulation by chromatin • Nucleosome positioning • Histone modification TF target site

13. DNA methylation H3K9me3 HP1 histone modification chromatin H3K9me3 H4K16ac

14. Epigenetic reprogramming during development • Methylation marks are erased during cleavage. • Methylation of the maternal genome is actively stripped within hours of fertilization. • Maternal genome is passively erased at a slower rate. • de novo methylation after implantation. • Another round of demethylation during differentiation. • DNA methylation is essential for development.

15. Epigenetic reprogramming can reverse tumorgenesis Hochelinger et al. Genes & Dev, (2004)

16. Cancer and histone modification Chin, Nature (1998)

17. Cancer and chromatin BRG1, the motor component of the SWI/SNF chromatin complex, is mutated in multiple cell lines (Wong et al. 2000) • prostate DU145; • lung A-427; • prostate TSU-Pr-1; • lung NCI-H1299; • breast ALAB; • lung NCI-H1299; • pancreas Hs 700T • … suggesting BRG1 may be a tumor repressor protein

18. Genomic-view of epigenetic regulation • How to detect genome-wide patterns of epigenetic markers? • How do epigenetic factors regulate genome-wide gene expression? • How is the distribution of genome-wide epigenetic markers regulated?

19. 1.Tile microarray • 20 bp offset, 50-mers • Chr III + 233 promoters 2.Hybridize • mononucleosomal DNA • vs naked genomic DNA 3.Compute Log (mononuc/genomic) Yuan et al.,Science, (2005)

20. Nucleosome positioning in yeast HIS3 MFA2 MATa MATa MATa nucs centromere predicted positioned nucs CHA1 literature positioned nucs fuzzy nucs Yuan et al.,Science, (2005)

21. Stereotyped pattern Average signal (aligned by ATG codon) shows regular pattern. 95% CI Log2 Ratio Aligned by ATG Distance to ATG Yuan et al.,Science, (2005)

22. Transcription factor binding sites (TFBSs) are likely to be nucleosome-depleted TFBSs tend to be nucleosome-depleted. Motif sites that are unbound in our condition but bound in other conditions also tend to be nucleosome depleted. Motif sites that are always unbound do not have nucleosome-depletion property. Yuan et al.,Science, (2005)

23. Histone modification in yeast Liu et al.,PLoS Biology, (2005)

24. Co-regulated histone modifications Liu et al.,PLoS Biology, (2005)

25. Nucleosome positioning in human Ozsolak et al.,Nat Biotech, (2007)

26. Histone modification in human Guenther et al.,Cell, (2007)

27. Distinct histone modification pattern in Embryonic Stem (ES) cells Gene ES cells contain both repressive and active markers ES Differentiated cell type 1 Differentiated cells contain either repressive or active markers but not both Differentiated cell type 2 Differentiated cell type n H3K27M: repressive H3K4M: active Bernstein et al.Cell (2006)

28. Euchromatin and heterochromatin http://respiratory-research.com

29. Large–scale chromatin domain Rinn et al.Cell (2007)

30. Large-scale chromatin domain ENCODE, Nature, 2007

31. Large-scale chromatin domain Closed Open ENCODE, Nature, 2007

32. Large-scale chromatin domain Closed Open ENCODE, Nature, 2007

33. DNA methylation in human Eckhardt et al.Nat Gen. (2007)

34. DNA-methylation pattern in human Eckhardt et al.Nat Gen. (2007)

35. Acetyl Ubiquityl Methyl Phosphoryl Histone modification Luger et al.Nature, (1997) Histone tails can be covalently modified in multiple ways at multiple sites Felsenfeld and Groudine, Nature, (2003)

36. Histone code hypothesis “… multiple histone modifications, acting in a combinatorial or sequential fashion on one or multiple histone tails, specify unique downstream functions …” ― Strahl and Allis, Nature, (2000)

37. Statistical assessment of the global impact of histone acetylation on gene expression • Integrative analysis using multiple genomic data resources (sequence, gene expression, histone modification) • Linear regression model yiexpression;Aijacetylation;Sipromoter sequence • Key is to estimate sequence dependent regulatory effects. Yuan et al.Gen Bio (2006)

38. Estimating sequence dependent regulation effects Linear regression model with transcription factor binding motifs Sijmotif score • Scan motif (MDscan, AlignAce) • Filter out insignificant motifs (RSIR) linear f(Si) Yuan et al.Gen Bio (2006)

39. Performance of the linear regression model

40. Performance of the linear regression model

41. Performance of the linear regression model

42. Cumulative effect of histone acetylation Test whether including quadratic interaction between different acetylation sites would improve model performance quadratic interaction p-value for quadratic interaction coefficients (gjk) statistically insignificant

43. Reading List • Strahl and Allis 2000; • Proposed histone code hypothesis • Bernstein et al. 2007 • An up to date review of epigenomics • Yuan et al. 2005; • Nucleosome positions in yeast • Yuan et al. 2006; • Statistical analysis of histone related gene expression.