The sequence complexity of nuclear total RNA and nuclear poly(A)+RNA from Drosophilathird-instar larvae was determined by hybridization of these RNAs to labeled single-copy DNA. At saturation, the nuclear poly(A)+-and total RNA hybridized to 11% and 22.5% of the single-copy DNA, respectively. The increase in complexity ofnuclear total RNA over that observed for nuclear poly(A)+RNA indicates the presence of a discrete class of nonadenylylated nuclear RNA molecules. The relationship between DNA sequences coding for nuclear RNA and mRNA was then determined by hybridization of nuclear total and poly(A)+RNA to DNA enriched for mRNA coding sequences. The results ofthese studies show that those single-copy DNA sequences that are represented in either the poly(A)+-or poly(A)-mRNA population are transcribed into RNA molecules that appear in the nuclear poly(A)+RNA population.It has been proposed that high molecular weight nuclear RNA serves several functions within the eukaryotic cell, the most widely accepted ofwhich is as a precursor to cytoplasmic mRNA (1). Although little direct evidence for this role existed for several years, recent advances in molecular techniques have resulted in the identification and characterization ofnuclear precursors for several specific mRNAs (2-5). In these studies, it has been clear that the mRNA sequences represent only a portion of the primary transcripts, and hence specific processing appears to be an essential feature and potential regulatory event in mRNA biogenesis. In lower eukaryotes (i.e., fungi) there is little or no difference in either the complexity or the size of the RNAs found in the nucleus and the cytoplasm (6, 7); in these systems the relationship between nuclear transcripts and translated mRNAs appears to be direct. In higher eukaryotes, where nuclear RNA is several times more complex than mRNA, the relationship between the nuclear and mRNA species is not as clearly understood. In mouse and rat brain (8, 9), RNA-DNA hybridization experiments clearly show that the polyadenylylated nuclear RNA population contains all of the polyadenylylated cytoplasmic RNA sequences. However, it is also clear that both the nuclear RNA and mRNA are composed of poly(A)+-and poly(A)-RNA populations (8)(9)(10). At present, the relationship between the nonadenylylated nuclear RNA and mRNA in these systems is unknown.In Drosophila, however, a recent observation by Lengyel et al. (11) clearly indicates that the transcribed region ofone ofthe major Drosophila heat shock puff sites, 93D, is represented almost exclusively by poly(A)-RNA in the cytoplasm, whereas it is represented by both poly(A)+-and poly(A)-RNA in the nucleus.In view ofthis fact, and because we have determined that the mRNA of Drosophila third-instar larvae is composed of both adenylylated and nonadenylylated species (12), we have measured the sequence complexity of poly(A)+-and total nuclear RNA present in these larvae. We report here that, as was observed in larval mRNA, the nuclear RNA is composed of both an adenyly...