Abstract. We report studies using an enhanced experimental system to investigate organization of nuclear pre-mRNA metabolism. It is based on the powerful genetic system and polytene nuclei of Drosophila. We observe (at steady state) movement of a specific premRNA between its gene and the nuclear surface. This movement is isotropic, at rates consistent with diffusion and is restricted to a small nuclear subcompartment defined by exclusion from chromosome axes and the nucleolus. Bulk polyadenylated nuclear pre-mRNA precisely localizes in this same subcompartment indieating that most or all pre-mRNAs use the same route of intranuclear movement.In addition to association with nascent transcripts, snRNPs are coconcentrated with pre-mRNA in this subcompartment. In contrast to constitutive splices, at least one regulated splice occurs slowly and may undergo execution remotely from the site of pre-mRNA synthesis. Details of our results suggest that retention of incompletely spliced pre-mRNA is a function of the nuclear surface.We propose a simple model-based on channeled diffusion-for organization of intranuclear transport and metabolism of pre-mRNAs in polytene nuclei. We argue that this model can be generalized to all metazoan nuclei. METAZOAN nuclei contain specific substructures implicated in pre-mRNA metabolism (see, for example, Fakan and Puvion, 1980; Lerner et al., 1981; McConnell et al., 1987;Lawrence et al., 1989;Spector, 1990;Fu and Maniatis, 1990;Carter et al., 1991; CarmoFonseca et al., 1991; Huang and Spector, 1991; Shermoen and O'Farrell, 1991;Wu et al., 1991;Xing and Lawrence, 1991;Li and Bingham, 1991;Kopczynski and Muskavitch, 1992). The capacity to extend these provocative observations is currently constrained by lack of a suitable genetic system for dissection of structure-function relationships and by inadequate convenience (EM) or resolution (light microscopy) among the various techniques for analysis of three dimensional organization in highly complex, compact nuclei.We report development of a new experimental system that both augments physical analytical techniques and permits application of a powerful genetic system. Our approach exploits resources uniquely available in Drosophila. First ,,o500) of an individual interphase chromatid are tightly synapsed in register to produce a giant, polytene chromosome (for review see Ashburner, 1989). In contrast to most diploid interphase chromosomes, individual polytene chromosome arms are readily identifiable as discrete structures in intact nuclei. Moreover, the simple arrangement of Drosophila chromosome arms is retained in these giant nuclei. Thus, polytene nuclei provide an "exploded" view of a simple nucleus. Under these conditions the relatively limited resolution of rapid, convenient light microscopic techniques is sufficient to allow clear visualization of relationships between extrachromosomal features and sites of pre-mRNA synthesis, Third, molecular genetic tools are available permitting construction of genes abundantly transcribed in polytene...

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The Drosophila suppressor-of-white-apricot [su(wa)] protein regulates/modulates at least two somatic RNA processing events. It is a potent regulator of its own expression. We report here new studies of this autoregulatory circuit. Among other things, our studies show the following. First, new evidence that su(wa) expression is autoregulated at the level of pre-mRNA splicing is reported. su(wa) protein represses accumulation of the fully spliced su(wa) mRNA encoding it and promotes accumulation of high levels of incompletely spliced su(wa) pre-mRNA. Second, the fully spliced su(wa) mRNA is sufficient for all known su(wa) genetic functions indicating that it encodes the sole su(wa) protein. Third, the incompletely spliced su(wa) pre-mRNAs resulting from autoregulation are not translated (probably as a result of nuclear retention) and apparently represent nonfunctional by-products. Fourth, the special circumstances of su(wa) expression during oogenesis allows maternal deposition exclusively of fully spliced su(wa) mRNA. Fifth, su(wa) protein immunolocalizes to nuclei consistent with its being a direct regulator of pre-mRNA processing. We discuss the implications of our results for mechanisms of splicing regulation and for developmental control of su(wa) expression.

We have attempted to analyze at the molecular level mutants previously determined as having intragenic lesions caused by X-ray mutagenesis. C. S. Aaron isolated 33 null mutations at the Adh locus and in collaboration with other investigators classified 23 as deletions. Of the eight mutants analyzed here, only two produced a detectable ADH protein using the two-dimensional electrophoresis technique. Restriction endonuclease and Southern blot analysis showed that three of the mutants were normal compared to the wild-type restriction pattern, with one of the three producing a mutant ADH protein. Among the five mutants that had altered restriction patterns, only one mutant produced a detectable mutant ADH protein. All the mutants produced a hybridizable mRNA when probed with the genomic clones, suggesting that the mutant phenotype was not due to transcriptional inhibition. Two probable explanations proposed for these observations are (1) mutations may be due to deletions of one or a few bases resulting in frameshifts to nonsense codons and premature termination of ADH peptide synthesis or (2) mutations may be a result of transitions to nonsense codons, again producing shortened ADH proteins. Those mutants producing a mutant polypeptide may have resulted from mutations to missense rather than nonsense codons. The five mutants showing an abnormal endonuclease Southern blot along with the 23 mutants previously shown to be deletions (28/33 or 85%) are associated with multiple DNA chain breaks. Although all of the DNA chain breaks are not necessarily associated with the mutant phenotype of the Adh locus, multiple DNA chain breaks are the most consistent characteristic of ionizing radiation damage to DNA.