You are studying epigenetic regulation of the Bdnf gene in mice and its associat

Question

You are studying epigenetic regulation of the Bdnf gene in mice and its association with memory. You train mouse B to avoid an adverse stimulus and then isolate genomic DNA from its brain. Mouse A is untrained and used as a control. You take the brain DNA samples and split each of them into two parts. One part is treated with sodium bisulfite and the other part is left untreated. You then perform PCR for the Bdnf locus and digest the PCR product with the restriction enzyme AccII that cuts DNA at the sequence CGCG. The digested DNA is then separated by agarose gel electrophoresis to obtain the following DNA fragments:

Mouse A (Bisulfite DNA)                        Mouse A (Untreated DNA)

21.2 kb                                          19.3 kb

7.4 kb                                            7.4 kb

5.8 kb                                            5.1 kb

5.7 kb                                            3.9 kb

4.9 kb                                            3.5 kb

3.5 kb                                            2.7 kb

2.2 kb

1.9 kb

1.8 kb

0.7 kb

Mouse B (Bisulfite DNA)            Mouse B (Untreated DNA)

19.3 kb                                          19.3 kb

7.4 kb                                            7.4 kb

5.7 kb                                            5.1 kb

5.1 kb                                            3.9 kb

4.9 kb                                            3.5 kb

3.5 kb                                            2.7 kb

1.9 kb                                            2.2 kb

0.7 kb                                            1.9 kb

1.8 kb

0.7 kb

How many AccII sites are found at the Bdnf locus?

a. 4

b. 6

c. 9

d. 10

e. 16

It says that the correct answer is c but why???

Explanation / Answer

Mice B is trained to avoid adverse stimulus, while mouse A is the control. This is just to tell us that the bdnf in each mouse would have a different methylation level. This is also evident from the difference in the number of DNA fragments obtained from PCR of bdnf locus of bisulfite treated part of the brain of each mouse. However, the most convincing hint is the number of DNA fragments seen in PCR, obtained from untreated brain - the number is the same - 10. Also, the sizes of the fragments are the same. This is more than enough evidence to prove that the number of restriction sites (AccII) in the bdnf locus is 9. A given DNA, when cut 9 times, would give 10 fragments. Therefore, the answer is c. 9.

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