INTRODUCTION The operational term ‘Nuclear Matrix’ defines a structure that resists treatment of nuclei with detergents, high salt buffers and nucleases and was first described by Berezney and Coffey (1974). The concept of a basic skeleton struc- ture within the cell nucleus was attractive with respect to the topological organization of those nuclear processes that require a defined temporal accessibility of distinct areas among the highly ordered eukaryotic chromatin. Accord- ingly, it has been shown that DNA replication (Jackson and Cook, 1986), transcription (Jackson and Cook, 1985), RNA-processing (Agutter, 1985) and UV-induced DNA repair (McCready and Cook, 1984) are transiently associ- ated with a nuclear remnant framework. Moreover, a vari- ety of enzymes and regulatory proteins have been shown to be tightly associated with the nuclear matrix (e.g. see Kaufmann et al., 1986; Kirsch et al., 1986; Waitz and Loidl, 1991; Karwan et al., 1990; Li and Roux, 1992; Verheijen et al., 1988). A number of genes have been shown to be associated with the nuclear matrix in their actively tran- scribed configuration (e.g. see Jost and Seldran, 1984; Andreeva et al., 1992). Recently, some of the internal matrix proteins, the nuclear matrins, have been character- ized, cloned and sequenced (Nakayasu and Berezney, 1991; Belgrader et al., 1991; Hakes and Berezney, 1991); these studies demonstrate that matrins have structural character- istics typical of regulatory DNA-binding proteins, which is a further indication of the essential role of matrix proteins in the regulation of nuclear processes. One of the main problems of nuclear matrix research during the last few years has been the tendency of each lab- oratory to establish its own unique protocol for nuclear matrix isolation, depending on whether biochemical, mor- phological or DNA studies were being performed. For this reason discrepant results were often difficult to interpret. In 1121 Journal of Cell Science 105, 1121-1130 (1993) Printed in Great Britain © The Company of Biologists Limited 1993 We have investigated biochemical and ultrastructural aspects of the nuclear matrix during the naturally syn- chronous cell cycle of Physarum polycephalum. The mor- phology of the in situ nuclear matrix exhibited signifi- cant cell cycle changes as revealed by electron microscopic examination, especially during the progres- sion of nuclei through mitosis and S-phase. In mitosis the interchromatin matrix was found to be retracted to the nuclear periphery; during S-phase this interchro- matin matrix gradually reassembled, concomitant with the reconstruction of a nucleolar remnant structure. During the G 2 -period no significant changes in matrix morphology were observed. The pattern of nuclear matrix proteins was invariant during the cell cycle; no cycle phase-specific proteins could be detected. In vivo labelling of plasmodia with [ 35 S]methionine/cysteine showed that only a few proteins are synthesized and assembled into nuclear matrix structures in a cell cycle- dependent way; the majority of proteins were synthe- sized almost continuously. This was also shown for nuclear lamins homologues. In contrast to bulk nuclear histones, those histones that remain tightly bound to the nuclear matrix were synthesized and assembled into nuclear structures in the very first hour of S-phase; assembly was terminated in mid-S-phase, indicating that nuclear matrix-bound chromatin is replicated early in S-phase. Comparison of the acetylation pattern of matrix-bound histone H4 with bulk nuclear H4 revealed a largely elevated acetate con- tent of matrix H4. The percentage of acetylated sub- species was entirely different from that in bulk nuclear H4, indicating that matrix-associated histones represent a subpopulation of nuclear histones with distinct prop- erties, reflecting specific structural requirements of matrix-attached chromatin. Key words: nuclear matrix, cell cycle, chromatin, mitosis, histones, histone acetylation, lamin, intermediate filament proteins, Physarum polycephalum, histone acetyltransferase, histone deacetylase SUMMARY Biochemical and morphological characterization of the nuclear matrix during the synchronous cell cycle of Physarum polycephalum Siegfried Lang 1, *, Thomas Decristoforo 1 , Werner Waitz 2 and Peter Loidl 1,† 1 Department of Microbiology and 2 Department of Physiology, University of Innsbruck, Medical School, Fritz-Preglstr. 3, A-6020 Innsbruck, Austria *Present address: Department of Pharmacology, Peter-Mayrstr. 1, A-6020 Innsbruck, Austria † Author for correspondence