Proteolysis is a form of the biological control providing fast physiological response to changing conditions of an environment. The goal of the present work was to analyze the localization of the Arg-X proteolysis in complexes of histones and non-histone proteins isolated from supra-molecular structures (nucleoplasm, chromatin, the nuclear matrix) of cell nuclei of mature wheat germs during induction of growth. Cell nuclei were isolated from germs, cleared, and then nucleoplasm, chromatin, nuclear matrix were extracted by increasing ionic strength of solution. From isolated supra-molecular structures, non-histone proteins were separated from histones by using ion exchange chromatography. The Arg-X proteolytic activity was assessed by cleavage of Arg-X bonds in the arginine-enriched protein protamine in all nuclear fractions. It was shown that in the coleoptile, which grows by cell elongation, Arg-X proteolysis activity was at the level of nuclear matrix structures, namely the linker histone HI and core histones, and in mesocotyls, Arg-X proteolysis activity was found in the core histones of the fraction of chromatin tightly bound to the nuclear matrix. A possible role of Arg-X proteolysis in the fine regulation of morphogenetic mechanisms occurring during seed germination is suggested.