• Introduction
• 26 min
  1. From DNA to proteins: the multiple levels of regulation

  • Prof. Panagiotis Tsonis
• Chromatin and DNA
• 44 min
  2. Chromatin architecture and alterations in the control of gene regulation

  • Prof. Jeffrey Hansen
• 43 min
  3. Nucleosome dynamics and remodeling

  • Prof. Jonathan Widom
• 25 min
  4. DNA replication

  • Prof. Smita Patel
• Transcription
• 47 min
  5. Nucleotide dependent functioning of bacterial enhancer binding proteins, activators of sigma54 RNA polymerase

  • Prof. Martin Buck
• 44 min
  6. Mechanisms of transcription: the eukaryotic pre-initiation complex

  • Prof. Michael Hampsey
• RNA (I)
• 38 min
  7. Pre-mRNA splicing

  • Prof. Timothy Nilsen
• 60 min
  8. Self-splicing intron RNAs: ribozymes, parasites and agents of genomic change

  • Prof. Anna Marie Pyle
• 47 min
  9. Polyadenylation of mRNA precursors: mechanism, regulation and connections with other cellular processes

  • Prof. James Manley
• 46 min
  10. mRNA capping

  • Prof. Aaron Shatkin
• RNA (II)
• 40 min
  11. Nonsense-mediated and Staufen1-mediated mRNA decay: related pathways of post-transcriptional control in mammalian cells

  • Prof. Lynne Maquat
• 40 min
  12. The silent revolution: an introduction to gene regulation by microRNAs

  • Dr. Frank Slack
• 50 min
  13. RNA editing: changing the code in plants, animals and parasites

  • Prof. Stephen Hajduk
• Proteins
• 18 min
  14. The principle of translation

  • Prof. Joachim Frank
• 17 min
  15. Translation initiation

  • Prof. Patrick Linder
• 47 min
  16. Elongation of protein synthesis: structural basis of the process of decoding

  • Prof. Marina Rodnina
• 40 min
  17. Elongation of protein synthesis: structural basis of the peptide bond

  • Prof. Marina Rodnina
• 44 min
  18. How do proteins fold and why?

  • Prof. Walter Englander
• 55 min
  19. Protein degradation

  • Prof. Alfred Goldberg
• Understanding Global Gene Expression
• 33 min
  20. Comparing transcriptomes of distant organisms: the comparative ENCODE resource 1

  • Prof. Mark Gerstein
• 22 min
  21. Comparing transcriptomes of distant organisms: models of gene expression 2

  • Prof. Mark Gerstein
• 47 min
  22. Protein networks and analysis of global gene expression

  • Dr. Trey Ideker
• Archived Lectures *These may not cover the latest advances in the field
• 42 min
  23. Chromatin and transcription

  • Prof. Roger Kornberg
• 40 min
  24. Nuclear organization and gene expression

  • Prof. David Spector
• 35 min
  25. Gene and protein microarrays: tools for gene discovery and function

  • Prof. Craig R. Tomlinson

Printable Handouts

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Navigable Slide Index

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.