Ordering of cosmid clones covering the herpes simplex virus type I (HSV-I) genome: a test case for fingerprinting by hybridisation

Multiplex Analysis Using cDNA Transcriptomic Profiling

DNA microarrays contain microscopic DNA spots attached to a solid surface. Each spot contains picomolar levels of a specific DNA probe sequence and hybridization to the corresponding gene products can be detected and quantitated through the use of fluorescently labeled target DNA. In this format, DNA microarrays can be used to measure the expression level of thousands of genes in a single experiment. Here, we present a method to detect the mRNA transcriptional changes in neuronal precursor cells following differentiation using high density cDNA microarrays.

Overview of DNA microarrays: types, applications, and their future

This unit provides an overview of DNA microarrays. Microarrays are a technology in which thousands of nucleic acids are bound to a surface and are used to measure the relative concentration of nucleic acid sequences in a mixture via hybridization and subsequent detection of the hybridization events. This overview first discusses the history of microarrays and the antecedent technologies that led to their development. This is followed by discussion of the methods of manufacture of microarrays and the most common biological applications. The unit ends with a brief description of the limitations of microarrays and discusses how microarrays are being rapidly replaced by DNA sequencing technologies.

Microarray technology: beyond transcript profiling and genotype analysis

Understanding complex functional mechanisms requires the global and parallel analysis of different cellular processes. DNA microarrays have become synonymous with this kind of study and, in many cases, are the obvious platform to achieve this aim. They have already made important contributions, most notably to gene-expression studies, although the true potential of this technology is far greater. Whereas some assays, such as transcript profiling and genotyping, are becoming routine, others are still in the early phases of development, and new areas of application, such as genome-wide epigenetic analysis and on-chip synthesis, continue to emerge.

Handling long targets and errors in sequencing by hybridization

Sequencing by hybridization (SBH) is a DNA sequencing technique, in which the sequence is reconstructed using its k-mer content. This content, which is called the spectrum of the sequence, is obtained by hybridization to a universal DNA array. Standard universal arrays contain all k-mers for some fixed k, typically 8 to 10. Currently, in spite of its promise and elegance, SBH is not competitive with standard gel-based sequencing methods. This is due to two main reasons: lack of tools to handle realistic levels of hybridization errors and an inherent limitation on the length of uniquely reconstructible sequence by standard universal arrays. In this paper, we deal with both problems. We introduce a simple polynomial reconstruction algorithm which can be applied to spectra from standard arrays and has provable performance in the presence of both false negative and false positive errors. We also propose a novel design of chips containing universal bases that differs from the one proposed by Preparata et al. (1999). We give a simple algorithm that uses spectra from such chips to reconstruct with high probability random sequences of length lower only by a squared log factor compared to the information theoretic bound. Our algorithm is very robust to errors and has a provable performance even if there are both false negative and false positive errors. Simulations indicate that its sensitivity to errors is also very small in practice.

Exploiting the genetic potential of polyketide producing streptomycetes

Streptomycetes are the most important bacterial producers of bioactive secondary metabolites such as antibiotics or cytostatics. Due to the emerging resistance of pathogenic bacteria to all commonly used antibiotics, new and modified natural compounds are required for the development of novel drugs. In addition to the classical screening for natural compounds, genome driven approaches like combinatorial biosynthesis are permanently gaining relevance for the generation of new structures. This technology utilizes the combination of genes from different biosynthesis pathways resulting in the production of novel or modified metabolites. The basis for this strategy is the access to a significant number of genes and the knowledge about the activity and specificity of the enzymes encoded by them. A joint initiative was started to exploit the biosynthesis gene clusters from streptomycetes. In this publication, an overview of the strategy for the identification and characterization of numerous biosynthesis gene clusters for polyketides displaying interesting functions and particular structural features is given.

An oligonucleotide fingerprint normalized and expressed sequence tag characterized zebrafish cDNA library

The zebrafish is a powerful system for understanding the vertebrate genome, allowing the combination of genetic, molecular, and embryological analysis. Expressed sequence tags (ESTs) provide a rapid means of identifying an organism's genes for further analysis, but any EST project is limited by the availability of suitable libraries. Such cDNA libraries must be of high quality and provide a high rate of gene discovery. However, commonly used normalization and subtraction procedures tend to select for shorter, truncated, and internally primed inserts, seriously affecting library quality. An alternative procedure is to use oligonucleotide fingerprinting (OFP) to precluster clones before EST sequencing, thereby reducing the re-sequencing of common transcripts. Here, we describe the use of OFP to normalize and subtract 75,000 clones from two cDNA libraries, to a minimal set of 25,102 clones. We generated 25,788 ESTs (11,380 3' and 14,408 5') from over 16,000 of these clones. Clustering of 10,654 high-quality 3' ESTs from this set identified 7232 clusters (likely genes), corresponding to a 68% gene diversity rate, comparable to what has been reported for the best normalized human cDNA libraries, and indicating that the complete set of 25,102 clones contains as many as 17,000 genes. Yet, the library quality remains high. The complete set of 25,102 clones is available for researchers as glycerol stocks, filters sets, and as individual EST clones. These resources have been used for radiation hybrid, genetic, and physical mapping of the zebrafish genome, as well as positional cloning and candidate gene identification, molecular marker, and microarray development.

Oligonucleotide micro-arrays for identification of unknown mutations: how far from reality?

The present review examines critically what has been published on oligonucleotide micro-arrays, from the point of view of detection of unknown mutations. We will first demonstrate the theoretical power of this new technique, and then argue that it is experimentally realistic. However, technical difficulties remain, and the proposed solutions for controlling the hybridisation specificity and for manufacturing the micro-arrays will be reviewed. Some are promising, but a complete integration of several of these solutions must be achieved before oligonucleotide micro-arrays become a universal tool for routine detection of unknown mutations. Nevertheless, sequence specific arrays should be available in the short term for the most frequently studied genes.

Construction of physical maps from oligonucleotide fingerprints data

A new algorithm for the construction of physical maps from hybridization fingerprints of short oligonucleotide probes has been developed. Extensive simulations in high-noise scenarios show that the algorithm produces an essentially completely correct map in over 95% of trials. Tests for the influence of specific experimental parameters demonstrate that the algorithm is robust to both false positive and false negative experimental errors. The algorithm was also tested in simulations using real DNA sequences of C. elegans, E. coli, S. cerevisiae, and H. sapiens. To overcome the non-randomness of probe frequencies in these sequences, probes were preselected based on sequence statistics and a screening process of the hybridization data was developed. With these modifications, the algorithm produced very encouraging results.

Preselection of shotgun clones by oligonucleotide fingerprinting: an efficient and high throughput strategy to reduce redundancy in large-scale sequencing projects

Large-scale genomic sequencing projects generally rely on random sequencing of shotgun clones, followed by different gap closing strategies. To reduce the overall effort and cost of those projects and to accelerate the sequencing throughput, we have developed an efficient, high throughput oligonucleotide fingerprinting protocol to select optimal shotgun clone sets prior to sequencing. Both computer simulations and experimental results, obtained from five PAC-derived shotgun libraries spanning 535 kb of the 17p11.2 region of the human genome, demonstrate that at least a 2-fold reduction in the number of sequence reads required to sequence an individual genomic clone (cosmid, PAC, etc.) can be achieved. Treatment of clone contigs with significant clone overlaps will allow an even greater reduction.

Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules

New mapping approaches construct ordered restriction maps from fluorescence microscope images of individual, endonuclease-digested DNA molecules. In optical mapping, molecules are elongated and fixed onto derivatized glass surfaces, preserving biochemical accessibility and fragment order after enzymatic digestion. Measurements of relative fluorescence intensity and apparent length determine the sizes of restriction fragments, enabling ordered map construction without electrophoretic analysis. The optical mapping system reported here is based on our physical characterization of an effect using fluid flows developed within tiny, evaporating droplets to elongate and fix DNA molecules onto derivatized surfaces. Such evaporation-driven molecular fixation produces well elongated molecules accessible to restriction endonucleases, and notably, DNA polymerase I. We then developed the robotic means to grid DNA spots in well defined arrays that are digested and analyzed in parallel. To effectively harness this effect for high-throughput genome mapping, we developed: (i) machine vision and automatic image acquisition techniques to work with fixed, digested molecules within gridded samples, and (ii) Bayesian inference approaches that are used to analyze machine vision data, automatically producing high-resolution restriction maps from images of individual DNA molecules. The aggregate significance of this work is the development of an integrated system for mapping small insert clones allowing biochemical data obtained from engineered ensembles of individual molecules to be automatically accumulated and analyzed for map construction. These approaches are sufficiently general for varied biochemical analyses of individual molecules using statistically meaningful population sizes.

Stabilizating effect of 5-nitroindole (universal base) on DNA duplexes immobilized on gel matrix

Effect of attachment of 1-(2-deoxy-beta-D-ribofuranosyl)-5-nitroindole (NIDR) to the ends of target sequence of oligonucleotides immobilized on gel micromatrix on stability of duplex formed by hybridization with DNA fragment was studied. It was shown that adjunction of NIDR to 5' as well as to 3' end results in increasing stability of duplexes although in the second case the extent of stabilization effect is essentially lower. Both 5' and 3' terminal NIDR exhibited no selectivity to the opposite base while the stabilizing effect depended dramatically on the nature of the adjacent base especially in the case of 5'-end-attached universal base. The neighborhood of purine bases decreased substantially the stabilizing effect of 5' terminal NIDR. In contrast with this, the stabilizing effect of 3' terminal NIDR was reduced only slightly by adjacent pyrimidine bases.

Comparison of clone-ordering algorithms used in physical mapping

In this paper, a number of existing and novel techniques are considered for ordering cloned extracts from the genome of an organism based on fingerprinting data. A metric is defined for comparing the quality of the clone order for each technique. Simulated annealing is used in combination with several different objective functions. Empirical results with many simulated data sets for which the correct solution is known indicate that a simple greedy algorithm with some subsequent stochastic shuffling provides the best solution. Other techniques that attempt to weight comparisons between nonadjacent clones bias the ordering and give worse results. We show that this finding is not surprising since without detailed attempts to reconcile the data into a detailed map, only approximate maps can be obtained. Making N2 pieces of data from measurements of N clones cannot improve the situation.

Partial thermodynamic parameters for prediction stability and washing behavior of DNA duplexes immobilized on gel matrix

Earlier we showed that reported in literature nearest-neighbor thermodynamic parameters describe poorly the thermal-induced behavior of DNA duplexes immobilized in gel. Here we present a complete set of partial thermodynamic parameters for all 10 nearest-neighbor interactions specially developed for duplexes immobilized in gel. This thermodynamic library allows to predict dissociation enthalpy and free energy of DNA duplex immobilized in gel matrix from its base sequence. The predicted values are in good agreement with the experimental ones. Dissociation enthalpy and free energy are needed for such application as (i) predicting relative stability of duplexes formed by DNA with oligonucleotides immobilized in cells of gel matrix; (ii) selecting optimal conditions for hybridization experiment; (iii) predicting washing curves and washing temperatures at irreversible temperature-stepped wash of DNA out of oligonucleotide gel matrix; (iv) selecting optimal conditions for washing gel matrix.

Random-breakage mapping method applied to human DNA sequences

The random-breakage mapping method [Game et al. (1990) Nucleic Acids Res., 18, 4453-4461] was applied to DNA sequences in human fibroblasts. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated calls, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with DNA probes recognizing the single copy sequences of interest. The Southern blots show a band for the unbroken restriction fragments and a smear below this band due to radiation induced random breaks. This smear pattern contains two discontinuities in intensity at positions that correspond to the distance of the hybridization site to each end of the restriction fragment. By analyzing the positions of those discontinuities we confirmed the previously mapped position of the probe DXS1327 within a NotI fragment on the X chromosome, thus demonstrating the validity of the technique. We were also able to position the probes D21S1 and D21S15 with respect to the ends of their corresponding NotI fragments on chromosome 21. A third chromosome 21 probe, D21S11, has previously been reported to be close to D21S1, although an uncertainty about a second possible location existed. Since both probes D21S1 and D21S11 hybridized to a single NotI fragment and yielded a similar smear pattern, this uncertainty is removed by the random-breakage mapping method.

On the consistency of a physical mapping method to reconstruct a chromosome in vitro

During recent years considerable effort has been invested in creating physical maps for a variety of organisms as part of the Human Genome Project and in creating various methods for physical mapping. The statistical consistency of a physical mapping method to reconstruct a chromosome, however, has not been investigated. In this paper, we first establish that a model of physical mapping by binary fingerprinting of DNA fragments is identifiable using the key assumption-for a large randomly generated recombinant DNA library, there exists a staircase of DNA fragments across the chromosomal region of interest. Then we briefly introduce epi-convergence theory of variational analysis and transform the physical mapping problem into a constrained stochastic optimization problem. By doing so, we prove epi-convergence of the physical mapping model and epi-convergence of the physical mapping method. Combining the identifiability of our physical mapping model and the epi-convergence of a physical mapping method, finally we establish strong consistency of a physical mapping method.

Optical mapping of lambda bacteriophage clones using restriction endonucleases

Optical mapping is an emerging single molecule approach for the rapid generation of ordered restriction maps, using fluorescence microscopy. We have improved the size resolution of optical mapping by imaging individual DNA molecules elongated and fixed onto derivatized glass surfaces. Averaged fluorescence intensity and apparent length measurements accurately determined the mass of restriction fragments 800 basepairs long. We have used optical mapping to create ordered restriction maps for lambda clones derived from the mouse pygmy locus.

Four strikes against physical mapping of DNA

Physical mapping is a central problem in molecular biology and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NP-complete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the k-consecutive ones problem for k > or = 2. These models have been chosen to reflect various features typical in biological data, including false-negative and positive errors, small width of the map, and chimericism.

Impact of the human genome project on medical practice

BACKGROUND

The Human Genome Project is a coordinated effort to define the human genetic blueprint. The goals include construction of a variety of maps of the human genome, including the identification and localization of all genes. The discovery of genes responsible for human diseases has had a significant impact on the practice of medicine.

METHODS

Methods for defining the human genome include cytogenetic, physical, and genetic mapping techniques. A variety of strategies have been used to identify human genes, especially those genes that are responsible for disease. Once a disease gene has been identified, this information can be used to develop new diagnostic and therapeutic procedures.

RESULTS

A number of disease genes have already been identified, leading to improved diagnosis and novel approaches to therapy. A new type of mutation, trinucleotide repeat expansion, has been found to be responsible for at least seven diseases with an unusual inheritance pattern.

CONCLUSIONS

Materials and technology generated by the Human Genome Project and related research have provided important tools for the diagnosis and treatment of patients afflicted with genetic diseases.

Cosmid assembly and anchoring to human chromosome 21

A human chromosome 21-specific cosmid library from the Lawrence Livermore National Laboratory has been analyzed by two complementary methods, fingerprinting and hybridization; 40% coverage of the entire chromosome 21 has been achieved. To prepare a contig pool, approximately 9300 cosmid clones randomly selected from the library were fingerprinted and automatically assembled into 467 overlapping sets by the fluorescence-tagged restriction fragment method. The average size of the overlapping sets was 9.5 cosmids with minimal tiling paths consisting of 5.4 cosmids with a 10-kb extension each. However, as many as 10% of overlaps within members were estimated to be false. For regional localization, we hybridized gridded arrays of cosmids with inter-Alu-PCR probes obtained from YAC clones and somatic cell hybrids and assigned 592 cosmids to 26 subregions of 21q. Of these, 371 clones were incorporated into 139 contigs, anchoring the total 1864 cosmids to the subregion. The remaining 221 clones were mapped as orphans. To correlate the cytogenetic, YAC, and cosmid maps on 21q, the translocation breakpoints of the chromosomes contained in the somatic cell hybrids were mapped with respect to the STS content of the YACs. From the gene cluster regions, 176 ribosomal and 25 alphoid clones were isolated by hybridization. Together, these sets of anchored contigs and cosmids will provide a valuable resource for construction of a high-resolution map and for isolation of genes of interest from chromosome 21.

Oligonucleotide arrays: new concepts and possibilities

Advances in solid-phase oligonucleotide synthesis and hybridization techniques have led to an incipient technology based on the use of oligonucleotide arrays. The inclusion of a large number of oligonucleotide probes within a single array greatly reduces the cost of their synthesis and allows thousands of hybridizations to be carried out simultaneously. The range of potential applications of oligonucleotide arrays was expanded by the realization that nucleic acids can be sequenced by hybridizing them to all possible oligonucleotides of a given length. Additional possibilities are offered by novel types of oligonucleotide arrays that are capable of parallel sorting, isolating, and manipulating thousands, and even millions, of nucleic acid species. Fields, such as site-directed mutagenesis, protein engineering, and recombinant DNA technology, would benefit from using these arrays. Further, these approaches could enable the analysis of entire genomes by preparing ordered fragment libraries, and by sequencing complex pools of nucleic acids, in a novel approach that provides long-range sequence information by generating nested nucleic acids and then surveying the oligonucleotides contained in the nested strands. This would allow large diploid genomes to be sequenced directly in a completely automated procedure that does not require fragment cloning or chromosome mapping.

The chimeric mapping problem: algorithmic strategies and performance evaluation on synthetic genomic data

The Human Genome Project requires better software for the creation of physical maps of chromosomes. Current mapping techniques involve breaking large segments of DNA into smaller, more-manageable pieces, gathering information on all the small pieces, and then constructing a map of the original large piece from the information about the small pieces. Unfortunately, in the process of breaking up the DNA some information is lost and noise of various types is introduced; in particular, the order of the pieces is not preserved. Thus, the map maker must solve a combinatorial problem in order to reconstruct the map. Good software is indispensable for quick, accurate reconstruction. The reconstruction is complicated by various experimental errors. A major source of difficulty--which seems to be inherent to the recombination technology--is the presence of chimeric DNA clones. It is fairly common for two disjoint DNA pieces to form a chimera, i.e., a fusion of two pieces which appears as a single piece. Attempts to order chimera will fail unless they are algorithmically divided into their constituent pieces. Despite consensus within the genomic mapping community of the critical importance of correcting chimerism, algorithms for solving the chimeric clone problem have received only passing attention in the literature. Based on a model proposed by Lander (1992a, b) this paper presents the first algorithms for analyzing chimerism. We construct physical maps in the presence of chimerism by creating optimization functions which have minimizations which correlate with map quality. Despite the fact that these optimization functions are invariably NP-complete our algorithms are guaranteed to produce solutions which are close to the optimum. The practical import of using these algorithms depends on the strength of the correlation of the function to the map quality as well as on the accuracy of the approximations. We employ two fundamentally different optimization functions as a means of avoiding biases likely to decorrelate the solutions from the desired map. Experiments on simulated data show that both our algorithm which minimizes the number of chimeric fragments in a solution and our algorithm which minimizes the maximum number of fragments per clone in a solution do, in fact, correlate to high quality solutions. Furthermore, tests on simulated data using parameters set to mimic real experiments show that that the algorithms have the potential to find high quality solutions with real data. We plan to test our software against real data from the Whitehead Institute and from Los Alamos Genomic Research Center in the near future.

Relational genome analysis using reference libraries and hybridisation fingerprinting

The genomes of eukaryotic organisms are studied by an integrated approach based on hybridisation techniques. For this purpose, a reference library system has been set up, with a wide range of clone libraries made accessible to probe hybridisation as high density filter grids. Many different library types made from a variety of organisms can thus be analysed in a highly parallel process; hence, the amount of work per individual clone is minimised. In addition, information produced on one analysis level instantly assists in the characterisation process on another level. Genetic, physical and transcriptional mapping information and partial sequencing data are obtained for the individual library clones and are cross-referenced toward a comprehensive molecular understanding of genome structure and organisation, of encoded functions and their regulation. The order of genomic clones is established by hybridisation fingerprinting procedures. On these physical maps, the location of transcripts is determined. Complementary, partial sequence information is produced from corresponding cDNAs by hybridising short oligonucleotides, which will lead to the identification of regions of sequence conservation and the constitution of a gene inventory. The hybridisation analysis of the cDNA clones, and the genomic clones as well, could potentially be expanded toward a determination of (nearly) the complete sequence. The accumulated data set will provide the means to direct large-scale sequencing of the DNA, or might even make the sequence analysis of large genomic regions a redundant undertaking due to the already collected information.

Parallel synthesis and analysis of large numbers of related chemical compounds: applications to oligonucleotides

This review presents methods for addressing the issue of molecular complexity in biological systems. Biomolecules immobilised on solid phases can be used to probe biological interactions. As a specific example, arrays of large numbers of oligonucleotides allow the analysis of DNA sequences and complex populations of DNA molecules. The specific embodiments of this new method are presented, research up to mid-1992 outlined and requirements for future development discussed.

Top-down construction of an ordered Schizosaccharomyces pombe cosmid library

A very rapid and efficient method for sorting and ordering large numbers of clones is presented. This top-down mapping approach divides the entire ordering problem into many smaller tasks and analyzes in parallel a gridded membrane array of clones by hybridization with probe pools. The strategy was tested on a 15-fold-coverage Schizosaccharomyces pombe cosmid library. About 1600 clones were assigned to chromosomes and to regions defined by the Not I and Sfi I restriction maps. Then, the clones were ordered into 20 contigs, which is consistent with statistical expectations for the degree of genome coverage used. The parallel ordering of clones and the computer-based analysis of digitized images make this approach very efficient; it is about 8-fold faster than existing methods. Only 61 hybridizations were needed to order 1600 clones.

Dissociation of duplexes formed by hybridization of DNA with gel-immobilized oligonucleotides

The method of DNA sequencing by hybridization with oligonucleotides matrix (SHOM) developed in this laboratory (1.2) uses the matrix of oligonucleotides immobilized within polyacrylamide gel. The particular feature of this matrix is that the apparent thermostability of the duplexes depends on the concentration of gel-immobilized oligonucleotides. This dependence is specific for oligonucleotides immobilized in the gel volume (3-D-immobilization) rather than on a flat surface of a filter or glass (2-D-immobilization). The theory has been developed that provides a quantitative description of temperature-dependent duplex dissociation within gel. The theory takes into account that the diffusion of dissociated DNA out of the gel is retarded by multiple acts of association-dissociation of DNA with immobilized oligonucleotides. It allows to calculate the apparent dissociation temperature of duplexes and describes quantitatively its growth upon increase in the enthalpy of duplex dissociation, concentration of immobilized oligonucleotides, gel thickness and decrease of dissociation entropy and washing time. Concentration of gel-immobilized oligonucleotides can be calculated for a normalized matrix in which GC-rich and AT-rich duplexes exhibit the same apparent thermostabilities and are washed off at the same temperature. This simplifies identification of perfect duplexes formed on the matrix which can be carried out for all duplexes at the same temperature. The gel-immobilized oligonucleotide matrix provides also a higher capacity for immobilization and therefore a higher sensitivity of measurements, resulting in a higher discrimination power for identification of perfect duplexes as compared with matrixes of oligonucleotides immobilized on a surface.

Selection of oligonucleotide probes and experimental conditions for multiplex hybridization experiments

Different DNA probes hybridize under different conditions. I examine the constraints of the design of oligonucleotide probes that are meant to hybridize to different unique sites in human genomic DNA under a single set of hybridization conditions as a parallel array. In 522 kb of human genomic DNA, 75% of 12-base and 89% of 22-base are unique, as opposed to 90% and 100% as expected of unstructured DNA, and this is not due solely to repetitive elements in the DNA. Hybridization in TMAC to reduce A+T content effects on melting temperature allows only 90% of unique targets to be hybridized under one set of conditions if a 2 degrees C difference between matched and mismatched sequences is required. Standard hybridization conditions allow no more than 60% of unique probes to be used together. This suggests that probe, hybridization conditions, and instrument design for multiple-probe hybridization applications will be harder than previously suggested.

A new bacteriophage P1-derived vector for the propagation of large human DNA fragments

We have designed a P1 vector (pCYPAC-1) for the introduction of recombinant DNA into E. coli using electroporation procedures. The new cloning system, P1-derived artificial chromosomes (PACs), was used to establish an initial 15,000 clone library with an average insert size of 130-150 kilobase pairs (kb). No chimaerism has been observed in 34 clones, by fluorescence in situ hybridization. Similarly, no insert instability has been observed after extended culturing, for 20 clones. We conclude that the PAC cloning system will be useful in the mapping and detailed analysis of complex genomes.

A physical and genetic map of the Stigmatella aurantiaca DW4/3.1 chromosome

A physical map of the myxobacterium Stigmatella aurantiaca DW4/3.1 chromosome was constructed by pulsed-field gel (PFG) long-range mapping. One-and two-dimensional pulsed-field gel analyses were used together with reciprocal double-restriction, cross-hybridization and hybridization fingerprint analysis. These PFG results were confirmed by Smith-Birnstiel analysis, by Southern hybridization using linking clones and clones of a lambda genomic library for the determination of adjacent restriction fragments and by transposon insertion mapping using defined genomic sequences for hybridization. It was thus possible to construct a circular restriction map of the single 9.35 Mbp chromosome of S. aurantiaca based on the endonucleases Asel and Spel. Genetic loci as well as the replication origin were located on the physical map by Southern hybridization using heterologous (derived from Myxococcus xanthus, Escherichia coli and Streptomyces lividans) and homologous probes that are mainly involved in development and cell motility.

Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe

A complete set of software tools to aid the physical mapping of a genome has been developed and successfully applied to the genomic mapping of the fission yeast Schizosaccharomyces pombe. Two approaches were used for ordering single-copy hybridisation probes: one was based on the simulated annealing algorithm to order all probes, and another on inferring the minimum-spanning subset of the probes using a heuristic filtering procedure. Both algorithms produced almost identical maps, with minor differences in the order of repetitive probes and those having identical hybridisation patterns. A separate algorithm fitted the clones to the established probe order. Approaches for handling experimental noise and repetitive elements are discussed. In addition to these programs and the database management software, tools for visualizing and editing the data are described. The issues of combining the information from different libraries are addressed. Also, ways of handling multiple-copy probes and non-hybridisation data are discussed.

Continuum of overlapping clones spanning the entire human chromosome 21q

A continuous array of overlapping clones covering the entire human chromosome 21q was constructed from human yeast artificial chromosome libraries using sequence-tagged sites as landmarks specifically detected by polymerase chain reaction. The yeast artificial chromosome contiguous unit starts with pericentromeric and ends with subtelomeric loci of 21q. The resulting order of sequence-tagged sites is consistent with other physical and genetic mapping data. This set of overlapping clones will promote our knowledge of the structure of this chromosome and the function of its genes.

The use of simulated annealing in chromosome reconstruction experiments based on binary scoring

We present a method of combinatorial optimization, simulated annealing, to order clones in a library with respect to their position along a chromosome. This ordering method relies on scoring each clone for the presence or absence of specific target sequences, thereby assigning a digital signature to each clone. Specifically, we consider the hybridization of oligonucleotide probes to a clone to constitute the signature. In that the degree of clonal overlap is reflected in the similarity of their signatures, it is possible to construct maps based on the minimization of the differences in signatures across a reconstructed chromosome. Our simulations show that with as few as 30 probes and a clonal density of 4.5 genome equivalents, it is possible to assemble a small eukaryotic chromosome into 33 contiguous blocks of clones (contigs). With higher clonal densities and more probes, this number can be reduced to less than 5 contigs per chromosome.

Mapping the whole human genome by fingerprinting yeast artificial chromosomes

Physical mapping of the human genome has until now been envisioned through single chromosome strategies. We demonstrate that by using large insert yeast artificial chromosomes (YACs) a whole genome approach becomes feasible. YACs (22,000) of 810 kb mean size (5 genome equivalents) have been fingerprinted to obtain individual patterns of restriction fragments detected by a LINE-1 (L1) probe. More than 1000 contigs were assembled. Ten randomly chosen contigs were validated by metaphase chromosome fluorescence in situ hybridization, as well as by analyzing the inter-Alu PCR patterns of their constituent YACs. We estimate that 15% to 20% of the human genome, mainly the L1-rich regions, is already covered with contigs larger than 3 Mb.

Evaluation of a cosmid contig physical map of human chromosome 16

A cosmid contig physical map of human chromosome 16 has been developed by repetitive sequence finger-printing of approximately 4000 cosmid clones obtained from a chromosome 16-specific cosmid library. The arrangement of clones in contigs is determined by (1) estimating cosmid length and determining the likelihoods for all possible pairwise clone overlaps, using the fingerprint data, and (2) using an optimization technique to fit contig maps to these estimates. Two important questions concerning this contig map are how much of chromosome 16 is covered and how accurate are the assembled contigs. Both questions can be addressed by hybridization of single-copy sequence probes to gridded arrays of the cosmids. All of the fingerprinted clones have been arrayed on nylon membranes so that any region of interest can be identified by hybridization. The hybridization experiments indicate that approximately 84% of the euchromatic arms of chromosome 16 are covered by contigs and singleton cosmids. Both grid hybridization (26 contigs) and pulsed-field gel electrophoresis experiments (11 contigs) confirmed the assembled contigs, indicating that false positive overlaps occur infrequently in the present map. Furthermore, regional localization of 93 contigs and singleton cosmids to a somatic cell hybrid mapping panel indicates that there is no bias in the coverage of the euchromatic arms.

Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models

An efficient method was developed for making complete sets of oligonucleotides of defined length, covalently attached to the surface of a glass plate, by synthesizing them in situ. A device carrying all octapurine sequences was used to explore factors affecting molecular hybridization of the tethered oligonucleotides, to develop computer-aided methods for analyzing the data, and to test the feasibility of using the method for sequence analysis. Further development is needed before the method can be used routinely, but our work shows that it has a number of potential advantages over gel-based methods: it should be easy to automate; the quality of the sequence results can be evaluated statistically; it provides a powerful way of comparing related sequences and detecting mutation; it can be applied to both DNA and RNA; and specific motifs can be incorporated into all sequences of the array to focus analysis on sequences of biological interest.

Analysis of the 5'-AAUAAA motif and its flanking sequence in human RNA: relevance to cDNA library sorting

The motif, N-8..N-1AAUAAAN1..N8 (where N is A, C, G or U), and its flanking sequence in human mRNA were examined by database analysis. Approximately 20% of 5'-AAUAAA in 3'-noncoding regions appear not to direct mRNA cleavage-polyadenylation. In coding regions, Asn-Lys, Ile-Lys and Ile-Asn are proven not to be unfavourable, and AAUAAA is not an unfavourable choice of coding sequence, occurring in 16% of mRNAs. Neither immediate flanking sequence nor associated motifs bear sufficient information content to account for the cleavage specificity observed. The unusual distribution and properties of the motif, AATAAA, in cDNA invite novel strategies for sorting cDNA libraries.

Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues

As part of an integrated mapping and sequencing analysis of genomes, we have developed an approach allowing the characterization of large numbers of cDNA library clones with a minimal number of experiments. Three basic elements used in the analysis of cDNA libraries are responsible for the high efficiency of this new approach: (1) high-density library arrays allowing thousands of clones to be screened simultaneously; (2) hybridization fingerprinting techniques to identify clones abundantly expressed in specific tissues (by hybridizations with labeled tissue cDNA pools) and to avoid the repeated selection of identical clones and of clones containing noncoding inserts; and (3) a computerized system for the evaluation of hybridization data. To demonstrate the feasibility of this approach, we hybridized high-density cDNA library arrays of human fetal brain and embryonal Drosophila with radiolabeled cDNA pools derived from whole mouse tissues. Fingerprints of the library arrays were generated, localizing clones containing cDNA sequences from mRNAs expressed at middle to high abundance (> 0.1-0.15%) in the respective tissue. Partial sequencing data from a number of clones abundantly expressed in several tissues were generated to demonstrate the value of the approach, especially for the selection of cDNA clones for the analyses of genomes based on expressed sequence tagged sites. Data obtained by the technique described will ultimately be correlated with additional transcriptional and sequence information for the same library clones and with genomic mapping information in a relational database.

W (A or T) sequences as probes and primers suitable for genomic mapping and fingerprinting

A limitation to the use of oligonucleotide probes as tools for genetic and physical mapping has been the low hybridization positive frequency obtained by oligonucleotides of sufficient length to hybridize preferentially to cloned insert DNA (and not host E. coli genomic DNA). Both computer and experimental results now indicate that oligonucleotide probes composed of W (A or T) sequence are preferentially found in eukaryotic DNA, and can be used to provide high frequency, discriminative hybridization. Such W sequences may be useful as either probes or PCR primers in molecular diagnostic applications as well as in genetic and physical mapping.

Optimized strategies for sequence-tagged-site selection in genome mapping

The physical mapping of complex genomes is based on the construction of a genomic library and the determination of the overlaps between the inserts of the mapping clones in order to generate an ordered, cloned representation of nearly all the sequences present in the target genome. Evaluation of the relative efficiency of experimental procedures used to accomplish this goal must minimally include a comparison of the fraction of the genome covered by the ordered arrays (or "contigs"), the average size of the contigs, and the cost, in terms of time and resources, required to generate the map. Sequence-tagged-site (STS) content mapping is one strategy that has been proposed and is being utilized for this type of experiment. This paper describes three STS selection schemes and presents computer simulations of contig-building experiments based on these procedures. The results of these simulations suggest that a nonrandom STS strategy that uses paired probes requires one-third to one-fourth as many STS assays as are required in random and nonpaired approaches, and also results in a map that has both greater genome coverage and a larger average contig size. This strategy promises to reduce the time and cost required to build a high-quality physical map.

Drosophila genome project: one-hit coverage in yeast artificial chromosomes

We present a strategy for assembling a physical map of the genome of Drosophila melanogaster based on yeast artificial chromosomes (YACs). In this paper we report 500 YACs containing inserts of Drosophila DNA averaging 200 kb that have been assigned positions on the physical map by means of in situ hybridization with salivary gland chromosomes. The cloned DNA fragments have randomly sheared ends (DY clones) or ends generated by partial digestion with either NotI (N clones) or EcoRI (E clones). Relative to the euchromatic portion of the genome, the size distribution and genomic positions of the clones reveal no significant bias in the completeness or randomness of genome coverage. The 500 mapped euchromatic clones contain an aggregate of approximately 100 million base pairs of DNA, which is approximately one genome equivalent of Drosophila euchromatin.

Use of high coverage reference libraries of Drosophila melanogaster for relational data analysis. A step towards mapping and sequencing of the genome

Three differently made, primary Drosophila cosmid libraries of 16-fold genome coverage have been generated. Also, a jumping library has been created by a new method that takes advantage of methylation differences between genomic DNA and vector. Thirdly, two cDNA libraries have been picked. All these libraries have been arrayed on high-density in situ filters, each containing 9216 clones. As a reference system, such filters are distributed and identified clones are provided. Single-copy probes have identified on average 1.4 cosmids per genome equivalent. Together with cytogenetically mapped yeast artificial chromosomes, the libraries are also being used for physically mapping the genome, mainly by oligonucleotide fingerprinting and pool hybridizations. cDNA clones are further examined by a partial sequencing analysis by oligomer hybridization.

Interspersed repetitive element polymerase chain reaction product mapping using a mouse interspecific backcross

We have developed a rapid method of generating and simultaneously mapping interrepeat polymerase chain reaction products using DNA from interspecific backcross animals derived from mating C57BL/6J and Mus spretus mice. This method is based on the high degree of B1, B2, and L1 dispersed repeat position polymorphism found between these two species of mouse. We have mapped 13 new loci to 9 different chromosomes and have found no evidence of clustering among these loci. The advantages of this approach are that no prior knowledge of sequence is required, a single PCR reaction generates many markers which can be mapped simultaneously, and only 50 ng of each backcross DNA (a finite resource) is required. We anticipate that many more markers remain to be characterized in this valuable new source of polymorphism.

A genome approach to the human X chromosome

The human X chromosome includes many disease genes, some of which have already been cloned using time-consuming and labor-intensive methods. A more efficient way to study this chromosome makes use of technology emerging from the human genome initiative.