Framework for a physical map of the human 22q13 region using bacterial artificial chromosomes (BACs)

Fosmid-based physical mapping of the Histoplasma capsulatum genome

A fosmid library representing 10-fold coverage of the Histoplasma capsulatum G217B genome was used to construct a restriction-based physical map. The data obtained from three restriction endonuclease fingerprints, generated from each clone using BamHI, HindIII, and PstI endonucleases, were combined and used in FPC for automatic and manual contig assembly builds. Concomitantly, a whole-genome shotgun (WGS) sequencing of paired-end reads from plasmids and fosmids were assembled with PCAP, providing a predicted genome size of up to 43.5 Mbp and 17% repetitive DNA. Fosmid paired-end sequences in the WGS assembly provide anchoring information to the physical map and result in joining of existing physical map contigs into 84 clusters containing 9551 fosmid clones. Here, we detail mapping the Histoplasma capsulatum genome comprehensively in fosmids, resulting in an efficient paradigm for de novo sequencing that uses a map-assisted whole genome shotgun approach.

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

A Schizosaccharomyces pombe artificial chromosome large DNA cloning system

The feasibility of using the fission yeast, Schizosaccharomyces pombe , as a host for the propagation of cloned large fragments of human DNA has been investigated. Two acentric vector arms were utilized; these carry autonomously replicating sequences ( ars elements), selectable markers ( ura4(+) or LEU2 ) and 250 bp of S. pombe terminal telomeric repeats. All cloning was performed between the unique sites in both vector arms for the restriction endonuclease Not I. Initially the system was tested by converting six previously characterized cosmids from human chromosome 11p13 into a form that could be propagated in S.pombe as linear episomal elements of 50-60 kb in length. In all transformants analysed these cosmids were maintained intact. To test if larger fragments of human DNA could also be propagated total human DNA was digested with Not I and size fractionated by pulsed field gel electrophoresis (PFGE). Fractions of 100-1000 kb were ligated to Not I-digested vector arms and transformed into S.pombe protoplasts in the presence of lipofectin. Prototrophic ura+leu+transformants were obtained which upon examination by PFGE were found to contain additional linear chromosomes migrating at between 100 and 500 kb with a copy number of 5-10 copies/cell. Hybridization analyses revealed that these additional bands contained human DNA. Fluorescent in situ hybridization (FISH) analyses of several independent clones indicated that the inserts were derived from single loci within the human genome. These analyses clearly demonstrate that it is possible to clone large fragments of heterologous DNA in fission yeast using this S.p ombe artificial chromosome system which we have called SPARC. This vector-host system will complement the various other systems for cloning large DNA fragments.

High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping

Large insert clone libraries have been the primary resource used for the physical mapping of the human genome. Research directions in the genome community now are shifting direction from purely mapping to large-scale sequencing, which in turn, require new standards to be met by physical maps and large insert libraries. Bacterial artificial chromosome libraries offer enormous potential as the chosen substrate for both mapping and sequencing studies. Physical mapping, however, has come under some scrutiny as being "redundant" in the age of large-scale automated sequencing. We report the development and applications of nonelectrophoretic, optical approaches for high-resolution mapping of bacterial artificial chromosome that offer the potential to complement and thereby advance large-scale sequencing projects.

Construction and characterization of a large-fragment chicken bacterial artificial chromosome library

A large-insert bacterial artificial chromosome (BAC) library has been constructed from male chicken genomic DNA using the new pBeloBAC11 vector. The library was prepared in two parts, such that two-thirds of the BAC library (2976 clones) had an average insert size of 490 kb (80 clones analyzed), after optimization of transformation and HMW DNA size-selection conditions. Fragments of increased average size were cloned by coupling a second size strategy using pulsed-field gel electrophoresis with optimized electroporation that favored transformation of Escherichia coli DH10B cells with very large plasmids. The initial one-third of this library (1440 clones) was constructed using the standard protocols and had an average insert size of 180 kb (40 clones analyzed). The overall library consists, at present, of 4416 clones with a combined insert size average of 390 kb (ranging from 25 to 725 kb). At least 95% of the BAC clones contain inserts. This is partially due to a second color selection performed with respect to white colonies, as well as to the optimized ligation conditions used. Based on the percentage of clones with inserts and the analysis of insert sizes, we estimate this library to represent a 0.8-fold coverage of the chicken genome. Southern blot analysis and fluorescence in situ hybridization were performed to confirm the identity of the BAC inserts with chicken genomic DNA. Analysis of large chicken BAC inserts showed that they were stably propagated for at least 120 cell generations. The results indicate that the BAC system is able to carry stably very large genomic fragments of chicken DNA, this system translating into a powerful tool for physical mapping and positional cloning of the chicken genome.

Retrofitting vectors for Escherichia coli-based artificial chromosomes (PACs and BACs) with markers for transfection studies

P1-based artificial chromosomes (PACs) and bacterial artificial chromosomes (BACs) have significantly expanded the size of fragments from eukaryotic genomes that can be stably cloned in Escherichia coli as plasmid molecules. Functional characterization of a gene within a given PAC or BAC clone often requires transferring the DNA into eukaryotic cells for transient or long-term expression. To facilitate transfection studies, we have developed protocols using the Notl restriction sites of any PAC or BAC clone to introduce a transfection reporter gene, lacZ, together with a selectable marker, neo. This enables transfected cells to be detected by X-Gal staining to verify DNA uptake, and clones of stably transformed cells may be selected for in the presence of the antibiotic G418. The same retrofitting protocols may be applied with other markers of interest to extend the functionality of PAC and BAC libraries, and specialized aspects of such manipulation of E. coli-based artificial chromosomes are outlined.

Cosmid-derived transcripts and sequence tags mapped to three subregions of human chromosome 22

Fifty cosmids from the ICRF, London, and Lawrence Livermore Laboratory, California, human chromosome 22 cosmid libraries were isolated, regionally assigned and tested for their ability to detect repeats or single copy sequences. The search resulted in nine cosmids containing repetitive motifs from the pericentric region of chromosome 22. An additional 19 cosmids, that detected single copy sequences in the long arm of chromosome 22q: 7 in the region 22q11.2-q13.1 and 12 in 22q13.1-qter, were mapped more precisely by fluorescence in situ hybridization. Three out of these 19 recombinants displayed restriction fragments containing (CA)n repeats, were subcloned and sequenced. One cosmid, representing a region coding for an ubiquitous 300-bp transcript, is localized 600 kb from PDGFB, and four cosmids contained sequences surrounding the ARSA gene at 22q13.3. Presently, long range physical maps, that may be useful for analysing structural alterations of chromosome 22q13, are being constructed from these additional, regionally assigned markers from chromosome 22q13 employing both existing cosmid and new bacterial artificial chromosome (BAC) libraries.