1. How are CHIP experiments performed? What are some of the limitations of the method?

2. How are CHIP assays quantitated? If the signal for a particular protein bound to DNA doubles in intensity, does this mean that the occupancy of the protein on DNA is doubled?

3. When a particular PCR signal vanishes, it is often interpreted as the protein in question dissociating from DNA. What are alternative explanations for this observation?

4. What is elutriation? What method did the authors devise to obtain a more highly synchronized cell population?

5. What data suggest that Swi/Snf and SAGA are not just bound constitutively along the chromosome awaiting signals from transcription factors to remodel chromatin?

6. What do histone acetylation and deacetylation do to chromatin structure? How would you probe this?

7. How might Ash1p antagonize the activity of Swi5p? How would you test your model?