1. Chromatin Structure & Gene Expression The Histone Code

2. Structural Features of DNA

3. The Genome is Organized into Chromosomes

4. A. Chromatin fibers exploding from lysed nucleus B. Metaphase Chromosome (folded fibers). DNA-Protein Fibers Make up Chromatin

5. Chromosomes Are made of Thick Chromatin Fibers

6. Thick Fibers Can Unravel to Reveal Thin Fibers

7. The Fundamental Chromatin Fiber is the 10 nm Fiber (DNA Associated With Nucleosomes) 30 nm fibers 10 nm fibers :“beads on a string” nucleosome DNA

8. Levels of DNA Packing Based on the Fundamental Fiber

9. Probing the 10 nm Fiber With Nuclease

10. Nucleosomes Are Composed of DNA and an Ocatamer of Four Histone Pairs + DNA

11. Nucleosome Structure DNA H2B H4 H3 H2A

12. H2A Fold H2A/H2B Dimer

13. Histones Assemble into Core Ocatamer

14. Final Ocatamer Assembly

15. Conformations for the 30 nm Fiber

16. Some Chromatin Allows Access to DNA By Specific Binding Proteins (TF & Pol)

17. Covalent Modification of the Histone Tails Can Alter DNA- Histone Interaction or “Mark” Nucleosomes Acetylation (lys) Methylation (Lys) Phosphorylation (ser) Ubiquination (Lys)

18. Chromatin is Dynamic- Remodeling Complexes Alter Structure or Positioning on DNA

19. A model for Dynamic Regulation of Chromatin & Access to DNA

20. Chromatin Remodeling Complexes Like Sir Can Recognize Acetylated Histone Tails

21. Heterochromatin Inactivates Specific Regions of Chromosomes With Defined Borders (Epigenetic Modification)

22. Variegated Position Effects Occur When Normally Active Genes Become Heterochromatin ~30-40 Loci modify PEV. Su(var) Genes suppress variagation. HDACs E(var) Genes enhance variagation Bromo & Chromodomain proteins Bromo domains bind Ac Chromo domains bind Me

23. Histone Modification May Mark Nucleosomes as Heterochromatin

24. Is There A Histone Modification Code?

25. David Allis’ Model For The Histone Code

26. Active Chromatin Can Become Extended in Looped Domains Locus Control Region (LCR)

27. Activation of Promoters By Acetylation & Phosporylation –The Standard Model A = Activator bound to upstream reg. seq. HAT = Histone Acetyl Transferase P = Phosphate Ac = Acetate Ki = Kinase Swi/SNF = Chromatin Remodeling Complex T = TATA Box M = Mediator

28. ChIP Assay

29. The Histone Code: What do we know for sure? The information required for proper gene transcription is not just the promotors enhancers and transcription factors Chromatin structure regulates gene expression Chromatin structure is regulated at different levels  Heterochromatin vs. Euchromatin  Nucleosome structure at promoters and other regulatory sequences Histone modification plays a role in the regulation of chromatin structure Modification of transcription factors also plays a role We can’t read the code yet!