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PubMed1991

Improved algorithms for searching restriction maps.

We present algorithms for searching a DNA restriction enzyme map for a region that best matches a shorter 'probe' map. Our algorithms utilize a new model of map alignments, and extensive experiments prove our model superior to earlier approaches for certain applications. Let M be the number of map sites and P be the number of probe sites. Our first algorithm, which optimizes only over a restricted class of alignments, requires O(MP log P) worst-case time and O(M + P) space. Our second algorithm, which optimizes over all alignments, runs in O(MP3) time and O(M + P2) space, under reasonable assumptions about the distribution of restriction enzyme cleavage sites. Combining the algorithms gives a map-searching method that optimizes over all alignments in O(MP log P) time in practice. The algorithms' effectiveness is illustrated by searches involving a genomic restriction map of Escherichia coli.

Algorithms↗

PubMed1989

An extended long-range restriction map of the human sex-determining region on Yp, including ZFY, finds marked homology on Xp and no detectable Y sequences in an XX male.

We have used pulsed-field gel electrophoresis to study the short arm of the Y chromosome by using a pseudoautosomal probe (MIC2Y) and adjacent Y-specific sequences 27a and 47z (DSXY5) in XX males and XY females, in order to detect chromosomal breakpoints which may have given rise to these individuals. The preliminary published long-range restriction map was used as a basis for this study. Our data confirm the reported fragment sizes and resolve some discrepancies. In addition, the recently cloned ZFY locus, pDP1007, the putative sex-determining locus, has been used to extend this long-range restriction map on Yp. Thus far, the X and Y copy of this sequence appear to have conserved GC islands around this locus, since it is found on a 280-kb fragment in males and females by using SacII, BssHII, NarI, and NotI. Only two Y-specific sequences of 50 and 70 kb have been detected at the pulsed-field level by using SfiI and NaeI, respectively. No translocation breakpoints have been detected in any of the patients studied. One XX male, GM1889, however, does not have any of the Y-specific fragments detected using conventional or pulsed-field gel electrophoresis. This is one of the few typical XX males who therefore does not have the ZFY copy of the TDF clone. Since all the other XX males hybridized to 47z, which is centromeric to ZFY, a series of DNA loci that are centromeric to 47z need to be studied in order to detect chromosomal breakpoints.

DNA Probes↗

PubMedDate not supplied

Preparation of a detailed restriction map of the avian leukosis virus MAV-2(O).

Unintegrated MAV-2(O) DNA was isolated from infected chicken embryo fibroblasts and inserted into the lambda bacteriophage vector lambda gtWES lambda B. Three x 10(6) bacteriophage plaques were screened, yielding a total of seven clones, six of which contained DNA representing the complete MAV-2(O) genome. Viral DNA was isolated from four of the clones and was used to transfect chicken embryo fibroblasts. All four clones produced virus as monitored by reverse transcriptase assay. When the four cloned viruses were inoculated into 10-day-old embryos, all hatched chickens developed osteopetrosis. One clone, lambda 9, induced osteopetrosis at a rate of onset and severity identical to that induced by the MAV-2(O) parental stock. This clone was selected for further study. To facilitate restriction mapping, the viral DNA from lambda 9 was subcloned into plasmid vector pUC 12 to construct a plasmid called p9. Cleavage of p9 DNA with single and multiple restriction endonucleases and hybridization with gene-specific probes identified the restriction fragments obtained. A comprehensive restriction map of cloned MAV-2(O) was generated and is compared with published maps and sequences of other avian retroviruses.

Animals↗

PubMed1986

Restriction maps and homologies of the three plasmids of Agrobacterium rhizogenes strain A4.

Agrobacterium rhizogenes strain A4 is a virulent agropine-type strain possessing three plasmids: plasmid a (pArA4a, 180 kb) is not necessary for plant transformation, plasmid b (250 kb) is the root-inducing plasmid (pRiA4), and plasmid c (pArA4c) is a cointegrate of pArA4a and pRiA4. The total plasmid DNA (pArA4) of strain A4 was cloned in the cosmid pHSG262 and the library obtained was used to establish BamHI maps of the three plasmids. The plasmids a and Ri have an apparently identical region and a partly homologous region, and are different in the remaining regions including their origins of replication. Another agropine-type A. rhizogenes strain, HRI, bears only one plasmid, which is the Ri plasmid (pRiHRI). pRiHRI and pRiA4 present the same restriction maps for a great part, but are different in a region of 48 kb; however, this region of pRiHRI is found unmodified in pArA4a and may have a role in the virulence of the bacteria. The comparison between the restriction maps of the plasmids of strain A4 leads us to propose that the recombination event leading to pArA4c formation occurs within the identical regions of pArA4a and pRiA4. In addition, the comparison with the already established map of pRiHRI suggests that strain HRI could have been derived from a recombination event between the two homologous regions of pArA4c with subsequent loss of the smaller plasmid.

Chromosome Mapping↗

PubMed1988

Avian nephroblastomas induced by a retrovirus (MAV-2) lacking oncogene. I. Construction of MAV-1 and MAV-2 proviral restriction maps and preparation of specific proviral molecular subclones.

A 9.8 kb DNA fragment containing the complete MAV-1 provirus was recloned from the recombinant bacteriophage lambda 311411 (Perbal et al., 1985) into the plasmid pAT153. A detailed and precise restriction map of the obtained clone (pAT-MAV-1) was constructed. From compilation of this map and the known sequence of a variable portion of the MAV-2 env gene was a restriction map of MAV-2 deduced. Knowledge of the detailed pAT-MAV-1 map facilitated the preparation of five specific proviral subclones: pAT-U3 and pUC-U3 (both contain the U3 domain of the proviral LTR, which is MAV-specific and displays no homology with other hitherto known retroviruses including avian endogenous proviruses), pUC-RU5 (containing the R and U5 domains of the proviral LTR), pUC-UT5 (containing untranslated sequences flanking the 5' LTR), and pUC-UT3 (containing untranslated sequences flanking the 3' LTR). Thus tools for analysis of integrated MAV-2 proviruses in nephroblastomas induced by this virus were formed.

Animals↗

PubMed1990

The complete AvrII restriction map of the Escherichia coli genome and comparisons of several laboratory strains.

The complete 13 site AvrII restriction map of the genome of E coli strain MG1655 is presented and compared with several other E. coli strains. The map was determined primarily by isolating individual AvrII fragments from pulsed-field gels, and hybridizing these large probes to a battery of mapped E. coli clones in lambda vectors. AvrII restriction patterns for eight other laboratory strains were determined and maps for seven of them deduced from the gel and comparisons between the strain genotypes, the MG1655 map, and AvrII sites in E. coli sequences taken from Genbank.

DNA Restriction Enzymes↗

PubMed1989

Restriction-map variation associated with the G6PD polymorphism in natural populations of Drosophila melanogaster.

Restriction-map variation was studied in 126 copies of the G6pd region in X chromosome lines of Drosophila melanogaster from North America, Europe, and Africa. Special attention was focused on the distribution of variation relative to the geographically variable polymorphism for two electrophoretic variants. Nucleotide heterozygosity as determined by eight six-cutter restriction enzymes for the 13-kb region is estimated, on the basis of the worldwide sample, to be 0.065%, which is the lowest value reported for any comparable region in the D. melanogaster genome. Significant linkage disequilibrium between electrophoretic alleles and restriction-site variation is observed for several sites. In contrast to published studies of other genetic regions, there are large insertions that reach significant frequencies and are found across considerable geographic distances. There is a clustering of this variation inside the first large intervening sequence of the G6PD gene.

Africa↗

PubMed1992

A contiguous Not I restriction map of band q22.3 of human chromosome 21.

A contiguous high-resolution NotI restriction map of the distal region of the long arm of human chromosome 21 was constructed by three strategies: linking clones to identify adjacent pieces of DNA, partial digestion to identify neighboring fragments, and cell line polymorphisms to prove identity or adjacency of DNA fragments. Twenty-nine single-copy DNA probes and five linking clone probes were used to determine the order of 30 Not I fragments, covering 10 megabases of DNA in band q22.3. Smaller Not I fragments occur preferentially in this region, suggesting that band q22.3 is unusually rich in genes, since Not I sites occur almost exclusively in CpG islands. Comparison of the physical map and genetic maps in this region reveals a 10-fold higher than average recombination frequency.

Animals↗

PubMed1985

Relationships of the Col plasmids E2, E3, E4, E5, E6, and E7: restriction mapping and colicin gene fusions.

Thirteen ColE plasmids representing the E2-E7 types have been compared by restriction mapping. Over 80% of their restriction sites were found to be similarly positioned, indicating that these plasmids share a common structure. Three variants are ColE2-CA42 and ColE7-K317, both of which contain 1.8-kb DNA segments in place of a 2.5-kb segment common to the other plasmids, and ColE6-CT14, which has an additional 5.0-kb DNA segment compared to the other plasmids. The colicin (col), immunity (imm), and colicin release (hic) genes of these plasmids have been localized to regions corresponding to those known for ColE3-CA38 and ColE2-P9, with the imm and hic genes adjacent to the 3' end of the col gene. Active colicin is produced from hybrid col genes containing 5' and 3' ends from different E-type plasmids. The 3'-termini of the fused col genes specify the colicin type.

Bacteriocin Plasmids↗

PubMed1989

Restriction-map variation at the zeste-tko region in natural populations of Drosophila melanogaster.

Restriction-map variation in 64 X chromosome lines extracted from three different natural populations of Drosophila melanogaster was investigated with seven six-nucleotide-recognizing enzymes for a 20-kb region including the zeste and tko genes. Ten restriction-site and four length polymorphisms (two insertions and two deletions) were detected. Contrary to the predicted lower level of variation for genes on the X chromosome, the level of variation attributable to nucleotide substitution (estimated heterozygosity/nucleotide = 0.004) was similar to that previously reported for autosomal loci. The amount of insertion/deletion variation in the studied region was within the range observed in autosomal regions and thus not explainable by a simple selection model against the effects of insertional mutations. A general lack of linkage disequilibrium between polymorphic sites was observed.

Animals↗

PubMed1989

Restriction mapping of rDNA and the taxonomy of Kluyveromyces van der Walt emend. van der Walt.

Ribosomal DNA from the type strains of 13 nomenspecies of Kluyveromyces and from other strains were mapped with 11 restriction endonucleases. The length of the repeating unit ranged from ca. 8.4 kb (in K. aestuarii) to ca. 10.9 kb (in K. phaffii). The length variation resided as expected in the nontranscribed spacer. The patterns confirmed some of the inferences articulated by various students of the genus. The closely related species K. marxianus and K. lactis constituted a core to which could be linked first K. wickerhamii and K. dobzhanskii and then K. aestuarii. The presumed relatedness between K. waltii and K. thermotolerans was endorsed by rDNA mapping as well, but evidence linking these two species to the rest of the genus is wanting. The restriction patterns suggest that the multispored species together with K. delphensis form a loose assemblage acting as a bridge between the "core" species and the species K. phaffii and K. lodderi.

DNA, Fungal↗

PubMed1992

Molecular cloning, sequencing and restriction mapping of the genomic sequence encoding human proacrosin.

In the present study, molecular cloning, sequencing and restriction mapping of the genomic sequence encoding human proacrosin is described. The full-length cDNA encoding human proacrosin was utilized to recover a 17-kb human genomic clone which was sequenced without further subcloning. The nucleotide sequences of the exons agree with the sequence of the cDNA reported previously. More than 500 bases of the promoter region were sequenced and found to be highly GC rich but devoid of an identifiable TATA box. These findings are generally consistent with a recently published report [Keime, S., Adham, I. M. & Engel, W. (1990) Eur. J. Biochem. 190, 195-200]. However, further sequence analysis revealed discrepancies between our clone and that previously reported. Sequencing of the first intron showed similarity with the published data for 54 bases of the 5' region, beginning with the donor splice site, and for 114 bases at the 3' end. However, 500 bases sequenced distal to the initial 54 bases at the 5' end of intron 1 showed no similarity with the published sequence. In addition, the boundaries of intron 3 differed such that a cytosine residue previously reported to be in exon 3 was found to be the first base of exon 4. Detailed studies were undertaken to confirm that our clone constitutes the authentic sequence of human proacrosin. Cloning and characterization of the human proacrosin gene may allow for informative studies of its regulation, and for a more detailed examination of its role in fertilization.

Acrosin↗

PubMed1978

Demonstration of three different subtypes of adenovirus type 7 by DNA restriction site mapping.

Restriction site mapping of the genomes of eight different isolates of adenovirus serotype 7 (Ad7) has been performed with six different restriction endonucleases. In this analysis, 37 different restriction sites were localized. Three distinctly different cleavage patterns of the genomes of the Ad7 strains were observed. These strains could not be distinguished by serological techniques. The following three subtypes were defined on the basis of their restriction site patterns: the Ad7 prototype, represented by strain Gomen originally isolated from a case of pharyngitis; subtype Ad7a, represented by the Ad7 vaccine strain and strains isolated from undifferentiated respiratory disease and from a healthy carrier; and a third subtype of Ad7, represented by three strains which were isolated from Swedish patients, all having pronounced clinical symptoms indicating severe systemic infection. A comparison of the restriction site maps of the protype of Ad3 and the three subtypes of Ad7 indicated greater differences in the position of restriction sites between strains of Ad7 than between strains of the two serotypes. This technique is consequently recommended to obtain a more precise definition of distinct entities of viruses.

Adenovirus Infections, Human↗

PubMed1988

The genome of the multicapsid baculovirus of Orgyia pseudotsugata: restriction map and analysis of two sets of GC-rich repeated sequences.

Five cosmids containing inserts that comprise the complete genome of the multicapsid nuclear polyhedrosis virus of Orgyia pseudotsugata were mapped with four restriction enzymes (Bg/II, ClaI, SstI, XhoI). From these cosmid maps, composite maps of the complete genome were constructed for each restriction enzyme. A region containing repeats of the sequence GGC downstream of the polyhedrin gene was used to probe the genome. It cross-hybridized with a region which, upon sequence analysis, was found to be a highly repetitive GC-rich region of nearly 500 nucleotides. The two GC-rich regions appeared to be evolutionarily unrelated.

Animals↗

PubMed1987

Restriction map of a capsule plasmid of Bacillus anthracis.

The capsule plasmid pTE702 of Bacillus anthracis has been physically mapped with the restriction endonucleases HindIII, PstI, BamHI, SalI, and XhoI. A HindIII fragment map of pTE702 (96.5 kb) was obtained by analysis of the recombinant plasmids and cosmids containing overlapping fragments partially digested with HindIII. The physical map for PstI, BamHI, SalI, and XhoI was obtained by double digestion mapping of these sites in relation to the HindIII sites. The replication region of pTE702 was determined by in vitro genetic replicon labeling in B. subtilis.

Bacillus anthracis↗

PubMed1992

PFGE-resolved RFLP analysis and long range restriction mapping of the DNA of Arabidopsis thaliana using whole YAC clones as probes.

The cleavage patterns of 23 rare-cutting restriction endonucleases (rcREs) on high molecular weight DNA, isolated from leaves of Arabidopsis thaliana (Arabidopsis), have been analysed using pulsed field gel electrophoresis (PFGE). The DNA digested with rcREs can be used for restriction fragment length polymorphism (RFLP) analysis. We show that RFLPs are more readily identified in restriction fragments that require resolution by PFGE than in smaller restriction fragments. Taking advantage of the low dispersed repetitive DNA content of the Arabidopsis genome, whole yeast artificial chromosomes (YACs) were used as probes to PFGE resolved genomic DNA. This enabled whole YAC clones to be used as RFLP markers and long range restriction maps to be constructed. These techniques should enhance the analysis of regions of the genome of Arabidopsis (and other organisms with low levels of dispersed repetitive DNA) that are the subject of chromosome walking strategies to isolate particular loci.

Arabidopsis↗

PubMed1978

Restriction map of the antibiotic resistance plasmid R1drd-19 and its derivatives pKN102 (R1drd-19B2) and R1drd-16 for the enzymes BamHI, HindIII, EcoRI and SalI.

The conjugative R plasmid R1drd-19, mediating antibiotic resistance to ampicillin (Ap), chloramphenicol (Cm), kanamycin (Km), streptomycin (Sm) and sulfonamides (Su) was mapped using the restriction endonucleases BamHI, HindIII, EcoRI and SalI. BamHI generates 5 fragments (A-E) with molecular weights between 46 x 10(6) 0.25 x 10(6) dalton, and HindIII 8(A-H) between 42 x 10(6) dalton (representing mainly the RTF) and 0.25 x 10(6) dalton (representing the main part of the RTF) and 0.1 x 10(6) dalton. EcoRI recognises 17 sites and produces fragments (A-Q) with molecular weights between 11.7 and 0.1 x 10(6) dalton. SalI yields 7 fragments (A-G) of 16.5 to 2.0 x 10(6) dalton. A physical map was constructed from fragments obtained by partial digestion of R1drd-19 with one restriction enzyme, by double and triple digestion of the DNA with two or three enzymes with and without isolation of individual bands from preparative gels. In addition the restriction patterns of several mutants of R1drd-19 were compared with it. Evidence is presented which indicates that the derivatives of R1 investigated are generated by extended deletions, namely the copy mutant pKN102 which has lost the Km resistance, R1drd-16, which has lost all resistances other than Km and the Kms derivative of R1drd-16, which represents the pure RTF. The map of R1drd-19 is remarkably different from those of R100 and R6-5. Its molecular weight was estimated to be 62.5 Md. The circular fragment order for BamHI is: A-C-B-D-E, for HindIII: A-D-C-B-F-H-E-G, for EcoRI: A-C-K-B-F-J-O-D-H-L-G-P-Q-N-I-E-M- and for SalI A-B-C-D-G-F-E.

Ampicillin↗

PubMed1989

Construction of a Not I restriction map of the fission yeast Schizosaccharomyces pombe genome.

Pulsed field gel electrophoresis and large DNA technology were used to construct a Not I restriction map of the entire genome of the fission yeast Schizosaccharomyces pombe. There are 14 detectable Not I sites in S. pombe 972h: 9 sites on chromosome I and 5 sites on chromosome II, while no Not I sites were found on chromosome III. The 17 fragments (including intact chromosome III) generated by Not I digestion were resolved by PFG electrophoresis. These fragments ranged in size from 4.5 kb to approximately 3.5 Mb. Various strategies were applied in determining, efficiently, the order of the fragments on the chromosomes. The genomic size measured by adding all the fragments together is about 14 Mb and the sizes of the three chromosomes are I, 5.7 Mb, II, 4.6 to 4.7 Mb, and III, 3.5 Mb. These are generally somewhat smaller than estimated previously.

Blotting, Southern↗