The nonchromatin structure of the nucleus has been prepared using a new strategy that preserves many specific associations of DNA and RNA with the matrix. Both matrix morphology and biochemical properties depend critically on the preservation of nuclear RNA and the preparation is termed the RNP-matrix. This structure selectively binds active chromatin and non-message hnRNA. We suggest that RNP-matrix plays a fundamental role in regulating patterns of gene expression and propose to study the molecular biology of its associated nucleic acids. The RNP-matrix morphology appears, in resinless sections, far better preserved than in preparation made by harsher procedures. All actively transcribed DNA sequences probed so far are tightly bound to the matrix, one third of the DNA sequences directly to the matrix proteins and the remainder linked to matrix hnRNP. HnRNA is separated into distinct classes: message precursor RNA is eluted as an RNP particle (prt-hnRNA) while non-message transcripts remain bound to the matrix (mtx-hn RNA). Cloned cDNA probes hybridize only to the prt-hnRNA while the cloned non-message HindIII l.9-kb repeat hybridizes only to mtx-hnRNA. The proteins of the RNP-matrix change radically with differentiation and serve as a marker for cell type. Transformation markedly alters matrix proteins with very different patterns resulting from onc gene transfection and from chemical carcinogenesis. (F)