The sequence specificity of micrococcal nuclease is not the cause of nucleosome depletion over Poly(dA:dT) elements.
(A) Shown is a standard sequence logo representation of the sequence specificity of micrococcal nuclease, as determined by aligning the ∼1,000,000 cut sites that we obtained in our study. In this standard representation, every position represents the probability distribution over the four possible nucleotides at that position (relative to the yeast genome composition), by the information content contained in that distribution. As can be seen, the information content is low, indicating that although micrococcal nuclease does have detectable sequence specificity, this specificity is low and can thus be found in nearly every small stretch of DNA in the yeast genome. (B) Shown is the ranking of all 4096 possible 6-mers by their preference to be cut by micrococcal nuclease, defined as the ratio between the probability that they appear as a cut site and the probability that they appear in the yeast genome. The top ranking 6-mers are shown, along with the (low ranking) position of AAAAAA and TTTTTT. (C) Shown is the fraction of micrococcal nuclease cut sites in which there is a Poly(dA:dT) element k basepairs away from the cut site, when k ranges from −100 bp (i.e., 100 bp inside the mapped nucleosome) to 250 bp (outside). For this analysis we took perfect Poly(dA:dT) elements of length 6 or greater. Note that the most likely position for Poly(dA:dT) elements is not at the cut site but rather ∼50 bp from the cut site.