Cellular fractionation of rat muscle. A, method schematic. Nuclei were first prepared from diced and homogenized rat leg muscle and cleaned of contaminating cellular structures by centrifugation first on isopycnic gradients and then on sucrose to float contaminating membranes while pelleting the denser nuclei. Crude NEs were prepared by digesting/extracting nuclear contents from isolated nuclei. Before MudPIT analysis, these were further extracted with 1% β-octyl glucoside and 400 mm NaCl or with 0.1 n NaOH to enrich for proteins associated with the insoluble Lamin polymer and integral membrane proteins, respectively. Microsomes/sarcoplasmic reticulum preparations were generated separately and analyzed for comparison/subtraction as they contain most expected membrane contaminants of the NE. B, top panel, before running both gradients, the crude nuclear fractions contained many chunks of myofibrillar material (e.g. Z-bands; highlighted with white arrowheads) released during homogenization. Bottom panels, after both gradients, isolated nuclei were clean of these contaminants. Phase-contrast light microscope images are shown. Scale bar, 10 μm. C, enrichment for NEs by chromatin digestion. DAPI staining for DNA visualizes significant nuclear chromatin content in an isolated muscle nucleus (left panels) and the loss of most of this material after two rounds of digestion with DNase and RNase each followed by salt washes (two right panels). Fluorescence microscope images are shown. Scale bar, 5 μm. D, ultrastructure of isolated NEs. Electron micrographs of crude muscle NEs show that most material in the population has the characteristic double membrane structure of the NE with little contamination from single membrane vesicles (a likely SR single membrane vesicle contaminant is highlighted by the white arrowhead). Arrows point to positions of NPCs. These NEs were further salt/detergent- or alkali-extracted prior to analysis by MudPIT. After such treatment, no structure remains that can be readily discerned by EM with the characteristics of NEs. Scale bar, 0.2 μm.