Question

You isolate nuclei from three different eukaryotic specis. You treat the samples in exactly teh same way (adding same amount of enzyme, buffer and time) to partially digest the chromatin with micrococcal nuclease, extract the DNA, and run it on a gel. You see the pattern below:

Lane	Approximate size of bands (in base pairs)
1	200, 400, 600, 800
2	180, 360, 540, 720
3	190, 380, 570, 760

1. Knowing that the core-DNA in all cell types is the same what is your explanation for the difference in size in the patterns you observe?

2. If you digested each of the three samples more thoroughly, what would the pattern look like? (Be specific and indicate what the size of the bands would be)

Answer 1

1) here chromatin is digested with MNase, MNase digests the exposed regions in the chromatin that is outside the core nucleosome,so it produces band corresponding to the length of DNA wrapped around the histone octamer, bands in the first lane are multiples of 200, this shows the length of DNA wrapped around the histone octamer is 200 bp, band of size 400 is produced when the cut is made after 2 nucleosomes and so on. In Lane 2 size of all bands is multiples of 180, so the length of DNA which wraps over the histone octamer is 180bp and for the lane, 3 sizes of bands are multiples of 190 so the length of DNA which wraps around histone octamer is 190bp.

2) if the Samples are digested more thoroughly MNase will digest around all nucleosomes so for sample 1 we will get a band of size 200bp, for sample 2 we will get a single band of size 180bp and for sample 3 we will get a single band of size 190bp.