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Results for “mapping insertion sites”

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PubMed1992

Oligonucleotide-directed site-specific mutagenesis in Drosophila melanogaster.

An efficient technique has been developed for performing in vivo site-directed mutagenesis in Drosophila melanogaster. This procedure involves directed repair of P-element-induced DNA lesions after injection of a modified DNA sequence into early embryos. An oligonucleotide of 50 base pairs, whose sequence spans the P-element insertion site, mediates base replacement in the endogenous gene. Restriction mapping, DNA sequencing, and polymerase chain reaction analysis demonstrate that base substitutions present in an injected oligonucleotide are incorporated into genomic sequences flanking a P insertion site in the white gene. This analysis suggests that progeny bearing directed mutations are recovered with a frequency of about 0.5 x 10(-3). Because Drosophila remains a premier organism for the analysis of eukaryotic gene regulation, this system should find strong application in that analysis as well as in the analysis of DNA recombination, conversion, repair, and mutagenesis.

Animals↗

PubMed1993

Analysis of the biased distribution of topoisomerase I break sites on replicating simian virus 40 DNA.

We previously mapped the locations of breaks introduced by eukaryotic topoisomerase I (topo I) in replicating simian virus 40 (SV40) DNA and observed an approximate 3:1 bias in the distribution of the break sites for the template strand for discontinuous DNA synthesis. In the present study, this bias has been confirmed by the mapping of additional sites utilizing a standard primer extension assay and a sensitive repetitive primer extension (RPE) method. No new sites could be detected on either strand of SV40 by the RPE method, despite the 10 to 20 fold greater sensitivity of the technique. To investigate the nature of the bias, a detailed analysis of the SV40 DNA sequence was undertaken. A set of 17 pentanucleotide sequences derived from those sites observed to be broken in the viral DNA extracted from SV40-infected cells define an in vivo consensus sequence. We show that the observed strand bias is likely due to the intrinsic asymmetric distribution of these consensus sequences on the two strands of SV40 DNA. To confirm these observations, double-stranded oligonucleotides containing previously identified in vivo topo I break sites were introduced in both orientations into SV40 to generate insertion mutants. Mapping experiments utilizing these mutants revealed that the inserted topo I break sites were broken in vivo regardless of their orientation, confirming that the SV40 sequence is the major, if not the sole determinant, of the observed strand bias. The possible origins of the strand bias are discussed in relation to the evolution of the virus.

Animals↗

PubMed1988

Recombination can initiate and terminate at a large number of sites within the rosy locus of Drosophila melanogaster.

This report presents the results of a recombination experiment designed to question the existence of special sites for the initiation or termination of a recombination heteroduplex within the region of the rosy locus. Intragenic recombination events were monitored between two physically separated rosy mutant alleles ry301 and ry2 utilizing DNA restriction site polymorphisms as genetic markers. Both ry301 and ry2 are known from previous studies to be associated with gene conversion frequencies an order of magnitude lower than single site mutations. The mutations are associated with large, well defined insertions located as internal sites within the locus in prior intragenic mapping studies. On the molecular map, they represent large insertions approximately 2.7 kb apart in the second and third exons, respectively, of the XDH coding region. The present study monitors intragenic recombination in a mutant heterozygous genotype in which DNA homology is disrupted by these large discontinuities, greater than the region of DNA homology and flanking both sides of the locus. If initiation/or termination requires separate sites at either end of the locus, then intragenic recombination within the rosy locus of the heterozygote should be eliminated. Contrary to expectation, significant recombination between these sites is seen.

Alleles↗

PubMed2006

Quantitative trait loci for locomotor behavior in Drosophila melanogaster.

Locomotion is an integral component of most animal behaviors and many human diseases and disorders are associated with locomotor deficits, but little is known about the genetic basis of natural variation in locomotor behavior. Locomotion is a complex trait, with variation attributable to the joint segregation of multiple interacting quantitative trait loci (QTL), with effects that are sensitive to the environment. We assessed variation in a component of locomotor behavior (locomotor reactivity) in a population of 98 recombinant inbred lines of Drosophila melanogaster and mapped four QTL affecting locomotor reactivity by linkage to polymorphic roo transposable element insertion sites. We used complementation tests of deficiencies to fine map these QTL to 12 chromosomal regions and complementation tests of mutations to identify 13 positional candidate genes affecting locomotor reactivity, including Dopa decarboxylase (Ddc), which catalyzes the final step in the synthesis of serotonin and dopamine. Linkage disequilibrium mapping in a population of 164 second chromosome substitution lines derived from a single natural population showed that polymorphisms at Ddc were associated with naturally occurring genetic variation in locomotor behavior. These data implicate variation in the synthesis of bioamines as a factor contributing to natural variation in locomotor reactivity.

Animals↗

PubMed1988

Comparisons of host cell DNA insertions and altered transcription at the site of insertions in few polyhedra bacilovirus mutants.

Few polyhedgra (FP) mutants of Autographa californica nuclear polyhedrosis virus (AcNPV) and the closely related strain Galleria mellonella (Gm)NPV have been reported which contain Trichoplusia ni host cell DNA sequences inserted into the viral genome between map units 35.0 and 37.7. New FP mutants are described with alterations of the HindIII-I restriction enzyme fragment (33.8 to 37.7 map units) of AcNPV, either deletions of viral DNA sequences or insertions of spodoptera frugiperda host cell DNA sequences. S. frugiperda DNA insertions from FP mutants were compared to T. ni host DNA insertions from FP mutants previously isolated (M.J. Fraser, G.E. Smith, and M.D. Summers (1983) J. Virol. 47, 287-300). Two host cell DNA sequences isolated from FP mutants, one of T. ni origin and one from S. frugiperda DNA, were transcribed in infected cells. Deletions of viral DNA sequences and insertions of host DNA sequences produce altered transcripts at the site of mutation as determined by both Northern and S1 nuclease analysis. Cell-free translation of cRNAs transcribed from wild-type viral DNA revealed an open reading frame coding for a 25-kDa protein at the site where host cell DNA insertions have been mapped. This was the same size as an infected-cell protein missing from most FP mutants examined.

DNA Transposable Elements↗

PubMed1984

Physical maps of SfMNPV baculovirus DNA and its genomic variants.

Spodoptera frugiperda MNPV was plaque-purified, and the viral DNA from the plaque-purified isolates was analyzed with restriction endonuclease enzymes. Seven distinct variants were identified when the DNA of the isolates were analyzed by EcoRI and HindIII. The DNAs of the SfMNPV predominant type (prototype) and the variants were mapped with BamHI, BglII, BstEII, EcoRI, HindIII, KpnI, and PstI by multiple enzyme digestion and blot hybridization. The cleavage sites generated by the seven restriction enzymes were ordered, and the sites were assigned map coordinates using a least-squares procedure. Since Autographa californica MNPV-E2 EcoRI fragment I, which contains the polyhedrin gene, hybridized with SfMNPV EcoRI fragment P, the physical map of SfMNPV was oriented with EcoRI P on the left, with site 1 being the EcoRI site between fragments F and P. The calculated genome size was 121.76 kilobase pairs or 80.36 X 10(6) Da. The DNA from each variant was compared to the DNA of the prototype for insertions, deletions, and new restriction sites. Physical maps were generated for each of the variants. The differences between the variant and the prototype were confined to four regions in the SfMNPV genome representing less than 16% of the prototype genome.

Chromosome Deletion↗

PubMed1986

Analysis of the vegetative replication origin of broad-host-range plasmid RK2 by transposon mutagenesis.

A range of Tn1723 transposon mutants of the oriV region of broad-host-range plasmid RK2 have been isolated, and the internal EcoRI fragment of the transposon has been deleted from each to reduce the insertion size from 9.6 kb (Tn1723) to 35 bp (delta Tn1723). Sequencing from the delta Tn1723-derived EcoRI site has allowed the precise mapping of these insertions to various points dispersed through the origin region. Using these mutants we have determined which regions of oriV RK2 are of functional importance to plasmid establishment following transformation of the host species Escherichia coli, Pseudomonas putida, and P. aeruginosa. Insertions into an A/T-rich region, and a region containing five direct repeat sequences prevented successful transformation of each host species tested, but the continuity of sequences adjacent to the five repeats were essential only in E. coli and P. putida. The establishment and maintenance in E. coli of a mini-RK2 replicon was found to be inhibited by transcription from an inducible promoter positioned to read into oriV RK2 against the direction of replication. Assays of transcription emerging from Tn1723 demonstrated significant levels from one end of the transposon only. Four mutants with insertions downstream of oriV RK2 were unable to become established in E. coli, and contained Tn1723 in the orientation which would supply transcription toward the oriV RK2 region. These results demonstrate both that the sequence requirements for oriV RK2 function differ between host bacterial species, and that origin function may be further influenced by the genetic environment in which it lies.

Base Sequence↗

PubMed2002

Ahi-1, a novel gene encoding a modular protein with WD40-repeat and SH3 domains, is targeted by the Ahi-1 and Mis-2 provirus integrations.

The Ahi-1 locus was initially identified as a common helper provirus integration site in Abelson pre-B-cell lymphomas and shown to be closely linked to the c-myb proto-oncogene. Since no significant alteration of c-myb expression was found in Abelson murine leukemia virus-induced pre-B-lymphomas harboring a provirus inserted within the Ahi-1 locus, this suggested that it harbors another gene whose dysregulation is involved in tumor formation. Here we report the identification of a novel gene (Ahi-1) targeted by these provirus insertional mutations and the cloning of its cDNA. The Ahi-1 proviral insertions were found at the 3' end of the gene, in an inverse transcriptional orientation, with most of them located around and downstream of the last exon, whereas another insertion was within intron 22. In addition, another previously identified provirus insertion site, Mis-2, was found to map within the 16th intron of the Ahi-1 gene. The Ahi-1 cDNA encodes a 1,047-amino-acid protein. The predicted Ahi-1 protein is a modular protein that contains one SH3 motif and seven WD40 repeats. The Ahi-1 gene is conserved in mammals and encodes two major RNA species of 5 and 4.2 kb and several other shorter splicing variants. The Ahi-1 gene is expressed in mouse embryos and in several organs of the mouse and rat, notably at high levels in the brain and testes. In tumor cells harboring insertional mutations in Ahi-1, truncated Ahi-1/viral fused transcripts were identified, including some splicing variants with deletion of the SH3 domain. Therefore, Ahi-1 is a novel gene targeted by provirus insertion and encoding a protein that exhibits several features of a signaling molecule. Thus, Ahi-1 may play an important role in signal transduction in normal cells and may be involved in tumor development, possibly in cooperation with other oncogenes (such as v-abl and c-myc) or with a tumor suppressor gene (Nf1), since Ahi-1 insertion sites were identified in tumors harboring v-abl defective retroviruses or a c-myc transgene or in tumors exhibiting deletion of Nf1.

Adaptor Proteins, Vesicular Transport↗

PubMed2002

The nature of quantitative genetic variation for Drosophila longevity.

Longevity is a typical quantitative trait: the continuous variation in life span observed in natural populations is attributable to genetic variation at multiple quantitative trait loci (QTL), environmental sensitivity of QTL alleles, and truly continuous environmental variation. To begin to understand the genetic architecture of longevity at the level of individual QTL, we have mapped QTL for Drosophila life span that segregate between two inbred strains that were not selected for longevity. A mapping population of 98 recombinant inbred lines (RIL) was derived from these strains, and life span of virgin male and female flies measured under control culture conditions, chronic heat and cold stress, heat shock and starvation stress, and high and low density larval environments. The genotypes of the RIL were determined for polymorphic roo transposable element insertion sites, and life span QTL were mapped using composite interval mapping methods. A minimum of 19 life span QTL were detected by recombination mapping. The life span QTL exhibited strong genotype by sex, genotype by environment, and genotype by genotype (epistatic) interactions. These interactions complicate mapping efforts, but evolutionary theory predicts such properties of segregating QTL alleles. Quantitative deficiency mapping of four longevity QTL detected in the control environment by recombination mapping revealed a minimum of 11 QTL in these regions. Clearly, longevity is a complex quantitative trait. In the future, linkage disequilibrium mapping can be used to determine which candidate genes in a QTL region correspond to the genetic loci affecting variation in life span, and define the QTL alleles at the molecular level.

Animals↗

PubMed1995

Computerized three-dimensional activation mapping study of spontaneous ventricular arrhythmias during acute myocardial ischemia in dogs. Evidence against macroreentrant mechanism.

This study was undertaken to investigate the activation patterns of spontaneous ventricular arrhythmias during acute myocardial ischemia in dogs. In 14 open-chest dogs, the left anterior descending coronary artery was occluded for 2 hours. Three-dimensional activation maps were derived from 240 bipolar sites by insertion of 60 plunge needle electrodes into both ventricles and the septum. Global ventricular activation sequences were displayed in five planes in 10 dogs, whereas the high density regional activation maps of the anterior wall were displayed in four layers in 4 dogs. Three-dimensional activation maps of 95 sinus beats, 82 premature ventricular complexes (PVCs), and 210 beats of ventricular tachycardia (VT) were analyzed. Sinus beats had a uniform activation pattern with total ventricular activation times measuring 42 +/- 4 ms and 67 +/- 8 ms during baseline and ischemia, respectively (P < .05). The PVCs and VTs originated from the subendocardial and intramural layers, and activation patterns invariably suggested focal excitation. Macroeentry was not operative because (1) the breakthrough sites were always remote from the latest activation areas; (2) there was no electrical activity bridging the gap between the termination of a beat and initiation of the subsequent beat; and (3) impulse conduction was not sufficiently delayed to reexcite the area of impulse origin even though functional conduction block was frequently present. In high-density regional activation maps, fragmented activity spanning the diastolic interval was never found. In conclusion, spontaneously occurring PVCs and VTs during acute myocardial ischemia in dogs display focal excitation with no evidence of macroreentry.

Animals↗

PubMed1990

Retroviral integration sites in transgenic Mov mice frequently map in the vicinity of transcribed DNA regions.

Transcription of cellular sequences flanking proviral insertion sites was studied in several Mov mouse strains, each of which carried one copy of the Moloney murine leukemia virus in its germ line. In three out of five randomly chosen Mov strains, the provirus had integrated in the vicinity of DNA regions transcribed in the embryonal stem cell line CCE and the embryonal carcinoma cell line F9. Assuming that CCE and F9 cells are developmentally equivalent to the early embryonic cells that were infected to establish the Mov strains, our results suggest that retroviruses integrate preferentially into actively transcribed DNA regions.

Animals↗

PubMed1985

Construction of nondefective adenovirus type 5 bearing a 2.8-kilobase hepatitis B virus DNA near the right end of its genome.

A novel helper-free adenovirus type 5 (Ad5) vector system, which utilizes a cloning site 0.2 kilobase (kb) from the right end of the genome, has been developed. To construct a nondefective Ad5 bearing the 2.8-kb DNA fragment of hepatitis B virus (HBV) at this site, we deleted the 2.1-kb nonessential E3 fragment from cloned DNA covering the right one-fourth of the Ad5 genome (76 to 100 map units), inserted the HBV DNA into this site, ligated the recombinant DNA to the rest of the Ad5 genome, and transfected the ligated DNA into human embryo kidney cells. Most of the recovered virus clones had only the E3 deletion and no HBV insertion, suggesting that a homologous recombination occurs between transfected DNAs in these cells. The isolated Ad5 virus bearing the HBV DNA (Ad5-HBL) grew without helper virus in HeLa cells as efficiently as wild-type Ad5, although the 1.9-kb major E4 transcript was detected only poorly in the early phase in the Ad5-HBL-infected cells, suggesting that the HBV DNA inserted upstream of the E4 promoter reduces the E4 transcript. HBV mRNAs transcribed from the inserted DNA were at least as abundant as Ad5 early mRNAs in the late phase of Ad5-HBL infection, but the HBV surface antigen was barely detectable in the infected-cell lysate and culture medium. This result suggests that HBV mRNAs can be transcribed from the inserted genes but no protein can be translated from the HBV mRNAs, presumably because of the translational suppression of cellular mRNAs caused by adenovirus in its late phase.

Adenoviridae↗

PubMed1988

A selective screen to recover chromosomal deletions and duplications in Drosophila melanogaster.

A screen is described that will select for breakpoints within a restricted chromosomal region in Drosophila. The aberrations recovered can be used to construct chromosomes carrying synthetic duplications and deletions. Such chromosomes have applications in the mapping of complementation groups at both the genetic and molecular level. In particular, breakpoints recovered after P element hybrid dysgenesis tend to be associated with P element insertion sites. Such aberration breakpoints can be genetically mapped, as synthetic deletions, and then used as transposon-tagged sites for the recovery of genomic clones.

Animals↗

PubMed1993

TTAA serves as the target site for TFP3 lepidopteran transposon insertions in both nuclear polyhedrosis virus and Trichoplusia ni genomes.

We have analysed TFP3 transposable elements from five independently isolated FP mutants of the Autographa californica nuclear polyhderosis virus (AcMNPV). We also analysed genomic copies of TFP3 elements amplified from the DNAs of the Trichoplusia ni cell line (TN-368) and T. ni larvae using the polymerase chain reaction (PCR). The sequences of all the newly isolated TFP3 elements closely resemble the previously described TFP3/1 element. Each of the transposons isolated from the virus mutants duplicated a TTAA tetranucleotide target site upon insertion into the viral genome. Four of these TFP3 elements transposed into three different 'TTAA' target sites within the 25 K gene (FP locus, map units 36-37 of AcMNPV). The fifth TFP3 element inserted at a 'TTAA' site within the AcMNPV Hin dIII-E fragment. One genomic TFP3 element, amplified from the TN-368 cell line DNA by an inverse PCR method, duplicated a 'TTAA' tetranucleotide target site that is present only once in the homologous larval DNA sequence. These data suggest that mobilization of TFP3 into both viral and cellular sites is identical in specificity and mechanism.

Animals↗

PubMed2004

Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry.

Protein interactions between MAP kinases and substrates, activators, and scaffolding proteins are regulated by docking site motifs, one containing basic residues proximal to Leu-X-Leu (DEJL) and a second containing Phe-X-Phe (DEF). Hydrogen exchange mass spectrometry was used to identify regions in MAP kinases protected from solvent by docking motif interactions. Protection by DEJL peptide binding was observed in loops spanning beta7-beta8 and alphaD-alphaE in p38alpha and ERK2. In contrast, protection by DEF binding to ERK2 revealed a distinct hydrophobic pocket for Phe-X-Phe binding formed between the P+1 site, alphaF helix, and the MAP kinase insert. In inactive ERK2, this pocket is occluded by intramolecular interactions with residues in the activation lip. In vitro assays confirm the dependence of Elk1 and nucleoporin binding on ERK2 phosphorylation, and provide a structural basis for preferential involvement of active ERK in substrate binding and nuclear pore protein interactions.

Amino Acid Sequence↗

PubMed1996

Simplified plasmid rescue of host sequences adjacent to integrated proviruses.

We have previously described a Moloney murine leukemia retroviral (MoMLV) vector useful for the generation of anchored long-range maps of complex mammalian genomes. We now report the development of a modified vector carrying the ColE1 origin of replication and the chloramphenicol-resistance (CmR) gene to facilitate the recovery of genomic sequences adjacent to integrated proviruses. We demonstrate the utility of this new vector for the rescue in plasmid form of a 6-kb human fragment containing portions of an Alu element adjacent to the proviral 3'-LTR from an infected human primary fibroblast clone. We generated a sequence-tagged site (STS) from the derived sequence outside the Alu element, and used a somatic cell hybrid mapping panel to assign this STS to human chromosome 10 by a polymerase chain reaction-based assay. We suggest that this new CmR vector will be useful for recovering sequences of genes interrupted by proviral insertion, to generate directional maps with respect to the inserted provirus using the single cleavage sites within the vector, and to generate site-specific STS for defining and mapping the integration site.

Animals↗

PubMed1983

The use of transposon insertion zdc-235::Tn10 (min 32) to clone and delete DNA from the terminus region of Escherichia coli.

Transposon zdc-235::Tn10 is inserted at min 32 on the genetic map of Escherichia coli, and we have used this transposon to clone 14 kb of DNA that flanks this insertion. The site of insertion of the transposon, and the restriction map of the cloned DNA, correspond well with the predictions of the Bouché restriction map for the terminus region (Bouché 1982). The zdc-235::Tn10 insertion, along with the zdd-230::Tn9 insertion, was used to obtain deletions of the region that has been cloned. Strains lacking a minimum of 14 kb, and more likely a minimum of 40 kb of DNA, showed no alteration of growth or cell morphology.

Chromosome Mapping↗

PubMed1982

Mapping of RNA polymerase binding sites in R12 derived plasmids carrying the replication-incompatibility region and the insertion element IS1.

Interactions between Escherichia coli RNA polymerase holoenzyme and three small plasmid DNAs (pSM1, pSM2, and pSM15) derived from the drug resistant factor R12 have been studied. These plasmids carry the copy number and incompatibility determinants, the origin of DNA replication and the rep gene(s) necessary for plasmid replication. They also contain the insertion element IS1 and the putative finO cistron. Thirteen DNA segments within the largest of the three plasmids (pSM2) were able to form either a binary and/or ternary complex with RNA polymerase. A unique strong binding site was mapped within the left end of IS1. Five binding sites were found within the rep-cop-inc region. Four of these are weak binding sites whereas the fifth does not form a stable binary complex and was detected by ternary complex formation. A strong binding site was located in the putative finO region whereas the remaining six binding sites are located in regions with unidentified genetic functions.

Base Sequence↗