A set of non-histone proteins has been identified in the nuclei from liver, brain, spleen and testis tissues of the rat. Following moderate digestion of thoroughly washed nuclei with DNase 1 or micrococcal nuclease, EDTA was added to 5 m M to the reaction mixture and the preparation centrifuged. We found that the supernatant contained a limited amount of non-histone proteins (fraction SI). Sodium dodecyl sulfate (SDS) gel electrophoresis revealed S1 to be composed of a remarkably simple set of proteins resolved into four groups (A -D) each possessing closely spaced doublets or a triplet. Their molecular weights were A, 76100-80000; B, 48200-49500; C, 44500-45200 and D, 39500-41 500. The yield suggested that these proteins were structural constituents; however, they did not coincide with the known structural proteins of the cell nucleus. Two-dimensional gel electrophoresis further resolved each of the SDS bands into as many as nine spots, according to various charges. Some were labelled with [32P]orthophosphate in vivo, or with [y-32P]ATP and purified nuclear protein kinase NII in vitro. The released proteins B -D had fairly constant relative molar ratios at various times of digestion, thereby indicating possible localizations a t similar sites in the nucleus. The kinetic data together with the aggregation property at neutral pH values and the solubility in 5 mM EDTA suggest that proteins B -D constitute a group of proteins that have several common characteristics.The abundance of protein species in the cell nucleus varies with the protein; some are structural or regulatory in function while others are catalytic in various biochemical processes. Isolation and characterization of these nuclear proteins should greatly aid in understanding the structure and function of the nucleus as well as the molecular properties of the protein in question. Isolation of a group of proteins which share molecular properties may be advantageous, as a common biological function may be involved. The precedent of this can be illustrated with histones and high mobility group (HMG) proteins. Histones, the building molecules of the nucleosomes [I], can be readily extracted in a set from the chromatin with dilute mineral acids [2]; H M G proteins, which confer a structural characteristic of the active Chromatin [3], are extracted as a group from chromatin with 0.35 M NaCl and remain soluble in 2There have been numerous studies on various nuclear architectures such as chromatin, nuclear matrix and nuclear envelopes. One approach is to use DNA-hydrolyzing enzymes ; for example, DNase I has been used to distinguish the transcriptionally active from the bulk chromatin in differential digestion kinetics [5], or to isolate the nuclear pore complexlamina fraction [6] and nuclear matrix [7].In our studies on nuclear proteins we were interested in protein components liberated from the nuclei by digestion with DNA-hydrolyzing enzymes. We report here that a novel and remarkably simple set of non-histone proteins was isolated from the nuclei by nucle...