Assignment 2

October 9, 2018

This assignment is worth 5% of the course grade.

Due in class, Tuesday Oct. 23.

To create a model system for studying chromatin folding and unfolding, a cell line was established for which two constructs were stably inserted at separate chromosomal loci:

an array of about 200 tandem copies of a 9 kb sequence. The 9kb sequence consists of the mouse mammary tumor virus (MMTV) promoter, driving the viral genes v-ras and BPV.
a gene encoding a chimeric protein NH3+-GFP-GR-COO- where GFP is the green fluorescent protein and GR is the glucocorticoid hormone receptor

Figure 2 shows that
a) In cells without hormone treatment, GFP-GR  protein fluorescence is only detected in the cytoplasm. Hybridization of the same slide with a v-ras/BPV probe (RNA-FISH) showed no transcript.
b) In cells treated with the corticosteroid hormone dexamethasone, GFP-GR is only found in the nucleus, while the v-ras/BPV transcript (circled) is seen as a bright signal against a background of fluorescence. The same cell, visualized at the appropriate wavelength for RNA flourescence, shows that the v-ras/BPV transcript is only present at a single locus.

Note: Some of these figures do not reproduce well in grayscale, so you need to either print in color or view them on a screen.

1) (1 point) State a plausible hypothesis that links the observations about the glucocorticoid receptor and the MMTV/v-ras/BPV genes.

2) (3 points) For each of the following figures, write 1 or 2 declarative sentences that state the key observation from the figure(s) ie. what is the "take home lesson"?
3) (1 points) Write a concise and precise discussion putting all the observations from parts 1 and 2 together. In other words, what were these experiments designed to show us about the relationship between chromatin structure and gene expression? Some analysis is requried here; simply restating what you said in 1 and 2 is not sufficient. Think of 1 and 2 as the Results, and part 3 as the Discussion.

Submitting your assignment

Note on grading: In assigning a grade, some consideration may be given to how the answer communicates your ideas. Keep in mind the following:

Note on academic integrity: The results shown in this assignment may be derived from the research literature. It will be considered a breach of academic integrity to search for the paper on the Internet and simply copy the author's conclusions from the paper.

Notes: If you have questions, it may help to send me a messge at