Separation of satellite DNA chromatin and main band DNA chromatin from mouse brain

Using restriction endonucleases which preferentially digest mouse main band DNA and leave satellite DNA intact, we have isolated highly purified chromatin fractions containing only mouse satellite or main band DNA. Following the digestion of mouse brain nuclei with EndoR Alu I, main band DNA chromatin is selectively extracted with 10mM Tris, 10mM EDTA. Satellite DNA chromatin is subsequently extracted from the nuclear pellet with Tris-3M urea and further purified on sucrose gradients. Chromatin extracted from digested nuclei with Tris-EDTA contains only main band DNA and has a molecular weight lower than 2 x 10(6). Chromatin fractions obtained from the lower regions of sucrose gradients of the Tris-Urea extracts contain 40--95% satellite DNA and have a molecular weight of 6 to 8 x 10(6). Both the satellite DNA and main band DNA chromatins contain all five histones and have a protein to DNA ratio of 1.3 to 1.