The specificity of the binding of purified non-histone proteins to DNA has been investigated through two types of experiments. Using a nitrocellulose filter assay at a low protein/DNA ratio, the binding of mouse non-histone proteins to mouse DNA was twice as great as the binding of mouse non histone protein to Drosophilu DNA. The reverse experiment using Drosophila nonhistone protein confirmed the interpretation that some protein . DNA complexes were specific. Protein . DNA complexes isolated by gel filtration chromatography indicated that 20% or 10% of the non-histone protein was bound to homologous or heterologous DNA respectively. Purified non-histone proteins bound with lower efficiency (1 5 %) than unpurified but with higher specificity to soluble chromatin than to naked DNA. This binding did not result from an exchange between chromatin non-histone proteins and purified non-histone proteins added in excess. DNA-bound and chromatin-bound proteins were analysed on polyacrylamide gels. Whereas no major qualitative differences were observed with DNA-bound proteins, some proteins bound to homologous mouse chromatin were different from those bound to heterologous Drosophila chromatin. These results suggest a possible role of DNA-bound non-histone proteins in the regulation of gene expression.In bacteria and viruses, the expression of genetic material has been shown to be controlled, at least partly, by DNA-binding proteins. Such regulatory mechanisms could exist in higher organisms. Nuclear non-histone proteins exhibit heterogeneity, specificity [ l -41, rapid turnover [5,6], modifications, e.g. phosphorylation [7,8] and hormone-binding [9,10], all of which are expected in molecules involved in gene regulation. Furthermore, several investigators have described the binding of non-histone protein to DNA [l 1 -191. The specificity of the protein-DNA interaction has been approached experimentally by the use of DNA-affinity chromatography [ l l , 14,16,17], sucrose gradient centrifugation [12,13,19] and filtration assay [15, IS]. By these different methods, it has been shown that there was a specificity in the formation of DNA . protein complexes.The addition of non-histone proteins to chromatin has been proposed to modify transcription in a manner characteristic of the tissue from which they were derived [20]. Several mechanisms could account forDNAase I or deoxyribonucleate 5'-oligonucleotidohydrolase (EC 3.1.4.5). this action. No direct correlation has been shown between the formation of DNA . protein complexes and the described effect of non-histone protein on chromatin transcription, since bound non-histone proteins have not been analysed for this effect.In this paper, we describe the binding of a class of non-histone proteins to native DNA and to chromatin. Dealing with a low protein/DNA ratio, we demonstrate a limited number of specific DNA binding sites in both cases. We also define conditions that should make it possible to isolate quantitatively the protein . DNA and protein . chromatin complexes.The experi...