Estimating genomic distance from DNA sequence location in cell nuclei by a random walk model

Visualization of elementary DNA replication units in human nuclei corresponding in size to DNA loop domains

Newly synthesized DNA in mammalian nuclei is concentrated in discrete nuclear granules called replication foci. These foci may be visualized using antibodies against 5-bromodeoxyuridine. In the early S-phase cells 100-250 foci are usually detected. On average, individual foci range between 0.5 and 2 microns in diameter and can be seen as clusters of more than ten average-sized (60-100 kb) synchronously activated replicons. In this study, employing minor modifications of the previous methods, we report the visualization of small replication foci of about 0.3 micron diameter (mini-foci). Some foci are clustered into folded chains consisting of 2-40 subunits. DNA content of one mini-focus is estimated to be 50-120 kb and there are 500-1500 mini-foci per cell in the early S-phase. Experimentally induced decrease in replicon size does not affect the size of mini-foci, suggesting that these represent elementary units of DNA replication in mammalian nuclei and are probably identical to the basic structural DNA loop domains.

Counting, measuring, and mapping in FISH-labelled cells: sample size considerations and implications for automation

Statistical models are used to investigate the need for automation in several potential areas of application of FISH-labelling techniques, including perinatal and tumour cytogenetics, genetic toxicology, and gene mapping. Predictions of the models, based on current estimates of likely error rates for spot-counting and measuring, suggest that a fully automated system is a realistic prospect for detecting full or high-level mosaic trisomies and that interactive systems have the potential to reduce substantially the human workload required to detect residual malignant disease or radiation-induced chromosome aberrations. There appear to be no foreseeable limits to the requirements for speed and accuracy in such systems, since there is effectively no lower limit to the level of relevant biological detail that can be investigated with these techniques.

Mapping and chromosome analysis: the potential of fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) is a method widely used for the delineation of chromosomal DNA. FISH is applied in many areas of basic research as well as in clinical cytogenetics. In this review important technical improvements as well as the various applications of this method are summarized. In the first part different labeling and detection procedures are described and the potential of various kinds of probes are discussed. Recent developments in optical instrumentation and digital imaging procedures are outlined in the second part. The following important applications of FISH are discussed: (a) new strategies for high resolution mapping of DNA sequences; (b) detection of chromosomal aberrations in clinical material; (c) techniques allowing the simultaneous detection of numerous probes by multiple color FISH; and (d) the new approach of comparative genomic hybridization, allowing a rapid and comprehensive analysis of chromosomal imbalances in cell populations, which is particularly useful for the cytogenetic analysis of tumor samples.

The DNA rearrangement associated with facioscapulohumeral muscular dystrophy involves a heterochromatin-associated repetitive element: implications for a role of chromatin structure in the pathogenesis of the disease

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant form of muscular dystrophy. The FSHD locus has been linked to the most distal genetic markers on the long arm of chromosome 4. Recently, a probe was identified that detects an EcoRI fragment length polymorphism which segregates with the disease in most FSHD families. Within the EcoRI fragment lies a tandem array of 3.2 kb repeats. In several familial cases and four independent sporadic FSHD mutations, the variation in size of the EcoRI fragment was due to a decrease in copy number of the 3.2 kb repeats. To gain further insight into the relationship between the tandem array and FSHD, a single 3.2 kb repeat unit was characterized. Fluorescence in situ hybridization (FISH) demonstrates that the 3.2 kb repeat cross-hybridizes to several regions of heterochromatin in the human genome. In addition, DNA sequence analysis of the repeat reveals a region which is highly homologous to a previously identified family of heterochromatic repeats, LSau. FISH on interphase chromosomes demonstrates that the tandem array of 3.2 kb repeats lies within 215 kb of the 4q telomere. Together, these results suggest that the tandem array of 3.2 kb repeats, tightly linked to the FSHD locus, is contained in heterochromatin adjacent to the telomere. In addition, they are consistent with the hypothesis that the gene responsible for FSHD may be subjected to position effect variegation because of its proximity to telomeric heterochromatin.

Long-range mapping of gaps and telomeres with RecA-assisted restriction endonuclease (RARE) cleavage

RecA-assisted restriction endonuclease (RARE) cleavage is a method to perform sequence-specific cleavage of genomic DNA, and is useful in physical mapping studies. After making two modifications, we have applied this method to mapping large regions of DNA in several cell types, including a notorious gap near the Huntington disease (HD) locus on chromosome 4. RARE cleavage fragments were analysed by pulsed field gel electrophoresis and Southern blotting and the distances between cleavage sites determined with accuracy. Using RARE cleavage, the gap measured was less than 60 kilobases in length. RARE cleavage is also a straightforward technique to map the distance from a marker to a telomere. The terminal 1.7 megabases of several HD and control cell lines were mapped with no large differences between cell lines in this region.

Kinetics of chromosome condensation in the presence of topoisomerases: a phantom chain model

We discuss the requirement of type II DNA topoisomerase in the process of mitotic chromosome condensation. Using a known model describing the collapse of homopolymers, we propose that the compaction process necessitates a change in the topological state (i.e., a self-knotting) of the chromosomal chain. We argue that the enzymes are necessary to reach the compact metaphase state in a time interval that is much smaller than the time expected in the uncatalyzed process. The folding process is such that the potential entanglement points are localized at particular regions of the chromosome known as the scaffold-associated regions. The concentration of entanglements in the metaphase chromosome is related to the average size of the radial loops. A phantom chain model for the condensation process, in which each potential entanglement point is dealt with by a topoisomerase II molecule, is proposed.

DNA stretching on functionalized gold surfaces

We describe a method for anchoring bacteriophage lambda DNA by one end to gold by Au-biotin-streptavidin-biotin-DNA bonds. DNA anchored to a microfabricated Au line could be aligned and stretched in flow and electric fields. The anchor was shown to resist a force of at least 11 pN, a linkage strong enough to allow DNA molecules of chromosome size to be stretched and aligned.

The 30 nm chromatin fiber as a flexible polymer

Our analysis of the data of van den Engh, Sachs, and Trask (Science 257, 1410 (1992)), for the dependence of the mean square distance between pairs of hybridization sites (< L2n >, micron 2) on the known genomic distance (n, bp) separating these sites on chromosome number 4 in G1 human fibroblast nuclei, shows that < L2n > is proportional to n2v with v = 3/5 for n < 1 Mbp. The v-value of 3/5 is characteristic of flexible polymer chains with excluded volume effects in dilute good solutions. Since the DNA concentration in nuclei is very high (ca. 1-10 mg/ml), and theory (Flory, J. Chem. Phys. 17, 303, 1949) predicts v = 1/2 for overlapping polymers, the finding of v = 3/5 means that the chromatin fibers do not overlap in interphase nuclei. The dependence of < L2n > on n for n < 4 Mbp is consistent with the model of large (approximately 6 Mbp, 3 microns diameter) loops of interphase chromatin attached to nuclear membrane sites. Using the constant (e.g., Widom, Ann. Rev. Biophys. Biophys. Chem. 18, 365 (1989)) and variable (Williams & Langmore, Biophys. J. 59, 606 (1991)) diameter fiber models, the Kuhn statistical segment of the 30 nm chromatin fiber was estimated to have a length of 196-272 nm with a corresponding DNA content of 21-37 kbp.(ABSTRACT TRUNCATED AT 250 WORDS)

Mapping of 386 kb of genomic DNA in the human dystrophin-encoding gene (DYS) using an ordered phage lambda sublibrary of a YAC clone containing the DYS region

An integrated restriction map for HindIII and EcoRI has been constructed for 386 kb of the human dystrophin-encoding gene by partial digest mapping of 35 overlapping lambda EMBL3cosW phage clones derived from a yeast artificial chromosome containing this region. Map construction was simplified in two ways. Firstly, the sequence arrangement of lambda EMBL3cosW is such that only map data from cloned inserts are generated using partial digests of lambda phage DNA asymmetrically labelled at the left cos end with a complementary 32P-labelled oligodeoxyribonucleotide. Secondly, the degree of partial digestion was standardised for each restriction enzyme by using ultraviolet light-induced formation of thymine dimers in the recognition sequence to partially block the cleavage reaction. The map provides the basis for work on the analysis of chromosomal rearrangements in this region which give rise to Duchenne muscular dystrophy, and for studies of chromosome structure and function.

Applications of molecular marker analysis to mosquito vector competence

A rapidly expanding cadre of molecular biology techniques is being developed for human and plant genetics, including development of the technology to identify large numbers of genetic markers and to evaluate these markers relative to phenotypic observations. In this review, David Severson discusses applications of these techniques for the analysis of mosquito vector competence.

Track structure, chromosome geometry and chromosome aberrations

The joint role of radiation track structure and chromosome geometry in determining yields of chromosome aberrations is discussed. Ideally, the geometric models of chromosomes used for analyzing aberration yields should have the same degree of realism as track structure models. However, observed chromosome aberrations are produced by processes on comparatively large scales, e.g., misrepair involving two DSB located on different chromosomes or two DSB separated by millions of base pairs on one chromosome, and quantitative models for chromatin on such large scales have to date almost never been attempted. We survey some recent data on large-scale chromosome geometry, mainly results obtained with fluorescence in situ hybridization ("chromosome painting") techniques. Using two chromosome models suggested by the data, we interpret the relative yields, at low and high LET, of inter-chromosomal aberrations compared to intra-chromosomal, inter-arm aberrations. The models consider each chromosome confined within its own "chromosome localization sphere," either as a random cloud of points in one model or as a confined Gaussian polymer in the other. In agreement with other approaches, our results indicate that at any given time during the G0/G1 part of the cell cycle a chromosome is largely confined to a sub-volume comprising less than 10% of the volume of the cell nucleus. The possible significance of the ratio of inter-chromosomal aberrations to intra-chromosomal, inter-arm aberrations as an indicator of previous exposure to high LET radiation is outlined.

The structure of human S-phase chromosome fibres

Recent in situ hybridization studies suggested that within the range of 0.1-1.0 Mb, human interphase chromosomes follow a random walk model (i.e. they behave as flexible polymers without major constraints). However, chromosome structure may differ in the G1, S, and G2 phases, and phase-specific constraints may be masked if the chromosome analysis does not discriminate between the phases. Therefore, using confocal microscopy, we examined the structure of S-phase chromosomes labelled with 5-iododeoxyuridine after prolonged treatment with 5-fluorodeoxyuridine. In the S-phase, labelled 0.32 mu chromosome fibres mostly appear as semi-circles with an average diameter of 0.83 +/- 0.03 mu. These semi-circles are joined together to form different 3D structures, and two semicircles frequently adopt s- or omega-like conformations involving about 2.5 mu of the chromosome contour length (L). Morphometric analysis of the S-phase fibres suggests that our data fit both the random flexible polymer model and also a model in which two constrained semi-circles are attached to each other by a flexible joint, thus eliminating constraints at long distances (L more than 2 mu).

Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping

A light microscope-based technique for rapidly constructing ordered physical maps of chromosomes has been developed. Restriction enzyme digestion of elongated individual DNA molecules (about 0.2 to 1.0 megabases in size) was imaged by fluorescence microscopy after fixation in agarose gel. The size of the resulting individual restriction fragments was determined by relative fluorescence intensity and apparent molecular contour length. Ordered restriction maps were then created from genomic DNA without reliance on cloned or amplified sequences for hybridization or analytical gel electrophoresis. Initial application of optical mapping is described for Saccharomyces cerevisiae chromosomes.

High resolution visual mapping of stretched DNA by fluorescent hybridization

We describe a method for stretching DNA, which, when combined with fluorescent hybridization procedures, forms a new mapping technology that produces a high resolution, vivid, multi-colour image and map. Restriction fragments and cosmid probes were successfully mapped by this procedure with validation by standard restriction mapping. A long range map of a > 200 kilobase region containing five copies of the amplified dihydrofolate reductase gene was easily generated within two days. This DNA mapping procedure offers a significant and rapid alternative to a variety of standard mapping procedures.

Polymer models for interphase chromosomes

The overall geometry of chromosomes in mammalian cells during interphase is analyzed. On scales larger than approximately 10(5) bp, a chromosome is modeled as a Gaussian polymer subjected to additional forces that confine it to a subvolume of the cell nucleus. An appropriate partial differential equation for the polymer Green's function leads to predictions for the average geometric length between two points on the chromosome. The model reproduces several of the experimental observations: (i) a square root dependence of average geometric distance between two marked chromosome locations on their genomic separation over genomic length scales from approximately 10(5) to approximately 10(6) bp; (ii) an approach of the geometric distance to a maximum value for still larger genomic separations of the two points; (iii) overall chromosome localization in subdomains of the cell nucleus, as suggested by fluorescent labeling of whole chromosomes and by radiobiological evidence. The model is also consistent with known properties of the 30-nm chromatin fiber. It makes a testable prediction: that for two markers a given number of base pairs apart on a given chromosome, the average geometric separation is larger if the configuration is near one end of the chromosome than if it is near the center of the chromosome.

Happy mapping: linkage mapping using a physical analogue of meiosis

We have devised a simple method for ordering markers on a chromosome and determining the distances between them. It uses haploid equivalents of DNA and the polymerase chain reaction, hence 'happy mapping'. Our approach is analogous to classical linkage mapping; we replace its two essential elements, chromosome breakage and segregation, by in vitro analogues. DNA from any source is broken randomly by gamma-irradiation or shearing. Markers are then segregated by diluting the resulting fragments to give aliquots containing approximately 1 haploid genome equivalent. Linked markers tend to be found together in an aliquot. After detecting markers using the polymerase chain reaction, map order and distance can be deduced from the frequency with which markers 'co-segregate'. We have mapped 7 markers scattered over 1.24 Mbp using only 140 aliquots. Using the 'whole-genome' chain reaction, we also show how the approach might be used to map thousands of markers scattered throughout the genome. The method is powerful because the frequency of chromosome breakage can be optimized to suit the resolution required.

Fluorescence in situ hybridization mapping of human chromosome 19: mapping and verification of cosmid contigs formed by random restriction enzyme fingerprinting

Automated restriction enzyme fingerprinting of 7900 cosmids from chromosome 19 and calculation of the likelihood of their overlap based on shared fragments have resulted in the assembly of 743 sets of overlapping cosmids (contigs). We have mapped 22% of the formed contigs (n = 165) and all of the contigs with minimal tiling paths exceeding 6 members (n = 50) to chromosomal bands by fluorescence in situ hybridization using DNA from at least one member cosmid. The estimated average size of the formed contigs is 60-70 kb. Thus, members of a correctly formed contig are expected to lie close to each other in metaphase and interphase chromatin. Therefore, we tested the contig assembly process by comparing the band assignment of two or more members selected from each of 97 contigs. Forty-two of these contigs were further characterized for valid assembly by determining the proximity of members in interphase chromatin. Using these tests, we surveyed a total of 431 joins counted along the minimal tiling path (280 in interphase as well as metaphase) and found 6 erroneous joins, one in each of 6 contigs (6% of tested).