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1. Introduction
2. DNA structure and folding
3. A problem of steric hindrance
4. A model for accessibility of nucleosomal DNA
5. Restriction enzyme digestion assay
6. Restriction enzymes access nucleosomal targets
7. Exposure depends on nucleosomal distance
8. Exposure depends on distance inside nucleosome
9. Uncoiling vs. sliding for a mononucleosome
10. Site exposure occurs without nucleosome sliding
11. Accessibility inside a chain of nucleosomes
12. Histone tail domains are often acetylated
13. Minor effects from histone acetylation
14. DNA-histone "bonds" occur every helical turn
15. Any protein can bind to DNA in a nucleosome
16. Site exposure and histone - DNA affinity(1)
17. Site exposure and histone - DNA affinity(2)
18. Invasion by collaborative competition
19. Cooperativity in gene activation inside nucleosome
20. FRET system analyzes nucleosome dynamics
21. FRET monitors distance to the closer acceptor
22. Efficient FRET from native nucleosomes
23. Nucleosomal conformations in salt solution
24. Histone subunits dissociate at elevated [NaCl]
25. Conformational change driven by acceptor (1)
26. Conformational change driven by acceptor (2)
27. FRET efficiency versus cation concentration
28. Two different explanations of FRET results
29. Equilibrium constant vs. salt concentration
30. Protein binding coupled to site exposure
31. DNA constructs
32. LexA binding causes conformational change (1)
33. DNA constructs
34. LexA binding causes conformational change (2)
35. LexA binding causes conformational change (3)
36. Rates of spontaneous site exposure
37. Measuring the rates of site exposure
38. Experimental system
39. Results from stopped flow experiment
40. Nucleosome dynamics analyzed by spectroscopy
41. Spectroscopy with donor dye only
42. Spectroscopy with donor and acceptor dyes
43. Rapid spontaneous site exposure in nucleosomes
44. A model for transcription through a nucleosome
45. Rapid spontaneous site exposure in nucleosomes
46. Bulged loop diffusion model
47. Bulged loop model for nucleosome remodeling
48. Summary of key messages

Topics Covered

• Chromatin composition
• Nucleosome structure and function
• Dynamic properties inherent to nucleosomes
• Invasion of nucleosomes by gene regulatory proteins
• DNA binding proteins and enzymes
• ATP dependent remodeling factors
• Nucleosome relocation

Links

Series:

• From DNA to Proteins

Categories:

• Cell Biology
• Genetics & Epigenetics

Talk Citation

Publication History

• Published on October 1, 2007

Financial Disclosures

• Prof. Jonathan Widom has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.