Abstract. Using a computer-based system for model building and analysis, three-dimensional models of 24Drosophila melanogaster salivary gland nuclei have been constructed from optically or physically sectioned glands, allowing several generalizations about chromosome folding and packaging in these nuclei. First and most surprising, the prominent coiling of the chromosomes is strongly chiral, with fight-handed gyres predominating. Second, high frequency appositions between certain loci and the nuclear envelope appear almost exclusively at positions of intercalary heterochromatin; in addition, the chromocenter is always apposed to the envelope. Third, chromosomes are invariably separated into mutually exclusive spatial domains while usually extending across the nucleus in a polarized (Rabl) orientation. Fourth, the arms of each autosome are almost always juxtaposed, but no other relative arm positions are strongly favored. Finally, despite these nonrandom structural features, each chromosome is found to fold into a wide variety of different configurations. In addition, a set of nuclei has been analyzed in which the normally aggregrated centromeric regions of the chromosomes are located far apart from one another. These nuclei have the same architectural motifs seen in normal nuclei. This implies that such characteristics as separate chromosome domains and specific chromosomenuclear envelope contacts are largely independent of the relative placement of the different chromosomes within the nucleus.E UKARYOTIC cells contain enormous lengths of DNA that must undergo considerable packing to fit inside the interphase nucleus. The packing is accomplished through multiple foldings of the DNA molecule within each chromosome and the folding of the chromosomes themselves inside the nucleus. This hierarchy of foldings is under several general constraints. First, the DNA must be available to regulatory factors and transcriptional machinery in such a way that readout of the genome can be precisely controlled. Second, the resident copies of DNA must be faithfully duplicated and repackaged with histones and other proteins; in dividing cells, the daughter helices must also be topologically resolved. Finally, nuclear division depends on a number of tightly orchestrated events: condensation of chromatin into compact chromosomes, dissolution of the nuclear envelope, movement of chromosomes to a central plate with subsequent splitting of daughter chromatids toward opposite poles, decondensation of daughter chromosomes, and reassembly of the nuclear envelope around them.Despite the interest in elucidating the means by which cells accommodate these constraints and package their genomes, only a meager sketch of higher order structures can currently be claimed. Beyond the level of the 10-nm nucleosomal fiber, little.consensus has been reached. This is particularly true of the highest level of chromosome organization, the threedimensional arrangement of chromosomes in the interphase nucleus. For reviews, see references 13 and 21.The giant ...

The bithorax complex (BX-C) of Drosophila, one of two complexes that act as master regulators of the body plan of the fly, is included within a sequence of 338,234 bp (SEQ89E). This paper presents the strategy used in sequencing SEQ89E and an analysis of its open reading frames. The BX-C sequence (BXCALL) contains 314,895 bp obtained by deletion of putative genes that are located at each end of SEQ89E and appear to be functionally unrelated to the BX-C. Only 1.4% of BXCALL codes for the three homeodomaincontaining proteins of the complex. Principal findings include a putative ABD-A protein (ABD-AII) larger than a previously known ABD-A protein and a putative glucose transporter-like gene (1521 bp) located at or near the bithoraxoid (bxd), infra-abdominal-2 (iab-2) boundary on the opposite strand relative to that of the homeobox-containing genes.

A computer-based system for recording and analysing light microscope images, combined with classical cytogenetic analysis, has revealed the spatial organization of the giant chromosomes of Drosophila salivary gland cells. Each polytene chromosome arm folds up in a characteristic way, contacts the nuclear surface at specific sites and is topologically isolated from all other arms.

Source code is available from ftp://saf.bio.caltech.edu/

SUMMARY The combination of optical fluorescence microscopy with digital image processing and analysis has been used to examine the three-dimensional organization of chromosomes within intact polytene nuclei. Although the arrangement indicates a high degree of flexibility, there are many conserved features between nuclei at the same developmental state. For example, chromosome arms are loosely coiled with centromeres clustered at the opposite end of the nucleus from the telomeres. Individual chromosome arms are not interwoven but occupy different spatial domains. Chromosomal sites that contact the envelope correlate with intercalary heterochromatin. Connections are observed between actively transcribing regions.