The three-dimensional chromosome topography in an intact nucleus has been determined using fluorescently stained Drosophila polytene chromosomes, optical fluorescence microscopy and newly developed, generally applicable, cellular image reconstruction techniques. The folding pattern is a complex mixture of parallel chromosomal segments and intertwined coils and shows extensive interaction of the chromosomes with the nuclear envelope.

Three-dimensional architecture of a polytene nucleus

The factors responsible for producing some degree of order to the arrangement of chromatin in the nucleus are reviewed. They are the following: 1. Chromosomes are attached to the nuclear membrane, nucleolus and intranuclear matrix. As a result they have a relatively fixed position in the nucleus. 2. In some species somatic pairing results in alignment of homologs. This is rare in mammals. 3. The association of ribosomal DNA and 5S DNA with the nucleolous results in the close approximation of the chromosomes carrying these DNA sequences. In man and other animals the most obvious consequence is satellite association. 4. Heterochromatin is condensed onto the inner nuclear membrane and periphery of the nucleolous while genetically active chromatin occupies the more central portion of the nucleus. The results is a peripheral location of late replicating DNA and a central location of early relicating DNA. 5. The DNA replication points tend to be associated with the nuclear matrix. Autoradiography of briefly labelled cells shows a high frequency of grains associated with nuclear matrix material. 6. Heterochromatin association results in chromocenters and ectopic pairing. 7. In addition to all these is the Rabl orientation or alignment of centromeres with centromeres and telomeres with telomeres. This polarization of the chromosomes results from the traction on the centromeres by the spindle fibers. There is no firm evidence for any higher degrees of order that might bring specific functioning genes into close proximity.

Arrangement of chromatin in the nucleus

It seems to be a rule of chromosome replication that heterochromatin synthesizes its DNA at a later stage than the rest of the chromosome.

Late DNA synthesis in heterochromatin.

Chromatin is thought to be structurally discontinuous because it is packaged into morphologically distinct chromosomes that appear physically isolated from one another in metaphase preparations used for cytogenetic studies. However, analysis of chromosome positioning and movement suggest that different chromosomes often behave as if they were physically connected in interphase as well as mitosis. To address this paradox directly, we used a microsurgical technique to physically remove nucleoplasm or chromosomes from living cells under isotonic conditions. Using this approach, we found that pulling a single nucleolus or chromosome out from interphase or mitotic cells resulted in sequential removal of the remaining nucleoli and chromosomes, interconnected by a continuous elastic thread. Enzymatic treatments of interphase nucleoplasm and chromosome chains held under tension revealed that mechanical continuity within the chromatin was mediated by elements sensitive to DNase or micrococcal nuclease, but not RNases, formamide at high temperature, or proteases. In contrast, mechanical coupling between mitotic chromosomes and the surrounding cytoplasm appeared to be mediated by gelsolin-sensitive microfilaments. Furthermore, when ion concentrations were raised and lowered, both the chromosomes and the interconnecting strands underwent multiple rounds of decondensation and recondensation. As a result of these dynamic structural alterations, the mitotic chains also became sensitive to disruption by restriction enzymes. Ion-induced chromosome decondensation could be blocked by treatment with DNA binding dyes, agents that reduce protein disulfide linkages within nuclear matrix, or an antibody directed against histones. Fully decondensed chromatin strands also could be induced to recondense into chromosomes with pre-existing size, shape, number, and position by adding anti-histone antibodies. Conversely, removal of histones by proteolysis or heparin treatment produced chromosome decondensation which could be reversed by addition of histone H1, but not histones H2b or H3. These data suggest that DNA, its associated protein scaffolds, and surrounding cytoskeletal networks function as a structurally-unified system. Mechanical coupling within the nucleoplasm may coordinate dynamic alterations in chromatin structure, guide chromosome movement, and ensure fidelity of mitosis.

Mechanical Continuity and Reversible Chromosome Disassembly Within Intact Genomes Removed From Living Cells

The solution secondary structures and nucleotide conformations in the telomeric DNA of Oxytricha nova have been determined by Raman spectroscopy. Structural polymorphism is demonstrated for both single-stranded [d(T4G4)4] and double-stranded [d(G4T4G4).d(C4A4C4)] telomere models. In the case of d(T4G4)4, which is a prototype for the single-stranded telomeric tail, an interquadruplex equilibrium involving parallel and antiparallel strand configurations is shown to be governed by the solution concentrations of both Na+ and K+. In both the parallel and antiparallel quadruplexes of d(T4G4)4, the local geometry of the phosphodiester backbone is similar to that of canonical B DNA, and associations between bases of the guanine quartet involve Hoogsteen hydrogen bonding. However, the deoxyguanosine (dG) sugar conformations are significantly different in the two quadruplexes. In the extended parallel form, dG residues assume only the C2'-endo/anti conformation with respect to deoxyribose pucker and glycosyl orientation. In the foldback antiparallel form, dG residues are distributed equally between C2'-endo/anti and C2'-endo/syn conformations. In the case of d(G4T4G4).d(C4A4C4), which serves as a model for the double-stranded B DNA regions of Oxytricha telomeres, we show that disproportionation of the B form duplex to yield stable parallel quadruplexes of the guanine-rich strand occurs reversibly at high solution concentrations of either Na+ or K+. The present study reveals that both interquadruplex and duplex-quadruplex conversions of Oxytricha telomeric DNA are under the control of an alkali cation switch.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural polymorphism of telomere DNA: interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy.

Flattened metaphase figures were obtained by squashing or air-drying cells from human leucocyte cultures that had been treated with colchicine and hypotonic sodium citrate prior to fixation. In such metaphase figures the Y chromosome was at the periphery of the figure more often than chance expectation and more often than the chromosome pairs 1, 2, or 16 or the chromosome groups 13–15, 17–18, 19–20, or 21–22. The Y chromosome was further from the center of circular metaphase figures than the mean value of all the chromosomes or the chromosome pairs 1, 2, or 3 or the chromosome groups 4–5, 6–12+X, 19–20 or 21–22.

Non-random distribution of chromosomes in metaphase figures from cultured human leucocytes. i. the peripheral location of the y chromosome.

Two collections of XY-containing karyotypes were screened to obtain every karyotype in which the Y chromosome was distinguishable from the other small acrocentric chromosomes. The metaphase figures co

Non-random distribution of chromosomes in metaphase figures from cultured human leucocytes. ii. the peripheral location of chromosomes 13, 17-18 and 21.

W.R. Breg

Papers

Non-random distribution of chromosomes in metaphase figures from cultured human leucocytes. i. the peripheral location of the y chromosome.

Non-random distribution of chromosomes in metaphase figures from cultured human leucocytes. ii. the peripheral location of chromosomes 13, 17-18 and 21.

Chromosome duplication in cultured leucocytes from presumptive xxx and xxxxy human subjects.