Immunlfluorescence staining and Western blotting of proteins from the nuclear extract fractions showed for the first time that protein TRITHORAX, one of the most important proteins maintaining the tissue-specific transcriptionally active state of many Drosophila melanogaster genes, is associated with the nuclear matrix. TRITHORAX displayed similar staining at different stages of nuclear extraction and on the polytene chromosomes of the intact nuclei, as well as after partial or complete disruption of the nuclear envelope and chromosome release. This suggests that TRITHORAX bound to certain regulatory chromosome regions interacts with the adjacent elements of the nuclear scaffold, i.e., links the regions of actively transcribed genes with the nuclear matrix.