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Results for “Sequence Deletion”

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At least 19 recordsLinked to original sources

PubMed1979

Nucleotide sequence deletions within the coding region for small-t antigen of simian virus 40.

Simian virus 40 early mutants with deletions mapping in the 0.53-0.60 region have been sequenced by the Maxam and Gilbert approach. All these deletions effect the small-t gene. The size of the shortened small-t-related polypeptides produced by several of the mutants has been compared with the molecular weight as deduced from the nucleotide sequence. There was good agreement for the mutants dl890, dl891, and dl2102. For dl2121 and dl2122 the small-t-related protein was considerably larger than expected. It is possible to explain this result on the basis of the nucleotide sequence: the normal splicing event of the small-t mRNA still occurs, but as the deletion shifts the reading frame, translation of the small-t-related polypeptide continues beyond the small-t splice, but in a different reading frame than large-T. Mutants dl883, dl884, and dl2112 have lost one of the small-t splicing boundaries, and no (or minute amonts of) small-t-related protein has been observed in mutant-infected cells. The possible relationship between splicing and transport of polyadenylic acid-containing mRNA from the nucleus to the cytoplasm in vertebrae cells is discussed.

Antigens, Viral↗

PubMed1976

Immunoglobulin allotypes of rabbit kappa chains: polymorphism of a control mechanism regulating closely linked duplicated genes?

The amino acid sequence of the constant (CK) region from the kappa immunoglobulin chains of a b9 rabbit is compared with the CK sequences, taken from the literature, of a b4 rabbit. These CK regions differ by 33% of their amino acid sequences and by three sequence insertions or deletions (sequence gaps). These extensive differences together with other published observations suggest that the b9 and b4 CK genes may not be simple alleles, but rather they may be encoded by closely linked CK genes present in every rabbit whose expression is regulated by a polymorphic control mechanism.

Alleles↗

PubMed1979

The nucleotide sequence of a DNA fragment from the replication origin of the antibiotic resistance factor R1drd19.

The recombinant plasmid pRK101 contains a DNA fragment which carries the complete replication origin of the antibiotic resistance factor R1drd-19 inserted into the vector plasmid pBR322. In a spontaneously arising mutant of this plasmid (pRK103) a deletion of about 215 base pairs (bp) has been detected by heteroduplex analysis and mapping with restriction endonucleases. Essential parts of the replication origin must be located in the deleted sequence. The deletion mutant pRK103, in contrast to its parent plasmid pRK101 is not replicated under the control of the R1 replicon, even when the R1 factor or copy mutants of it are present within the same cell. These latter plasmids can complement a plasmid-specific protein not coded by pRK101 but essential for R1-directed replication. The nucleotide sequence of a 252 bp HpaII fragment covering about 170--200 bp of the deletion was determined. This piece of DNA is rich in G and C and contains a series of small palindromes, symmetrically arranged repeated sequences and short selfcomplementary structures which may be of significance for the initiation of the DNA replication. The possiblity that the sequenced DNA fragment comprises a major part of the replication origin of R1drd-19 is discussed.

Base Sequence↗

PubMed1978

Determination of the endpoints of partial deletion mutants of the attachment site of bacteriophage lambda by DNA sequencing.

The deletion mutants b508 and b522 of bacteriophage lambda both end within the attachment site. The formation of such deletions is dependent upon the presence of intact integrase, and thus the deletion endpoints may be related to the normal crossover site in site-specific recombination. We have determined the DNA sequences of the attachment site regions of these deletions. Comparison of the sequences with lambda wildtype shows that both the deletions end within the central common homology region but at different positions. The consequences of these findings for current models of site-specific recombination are discussed.

Base Sequence↗

PubMed2025

Elimination of myotonia improves myopathy in a muscleblind knockout model of myotonic dystrophy.

A cardinal sign of myotonic dystrophy type 1 (DM1) is slow of muscle relaxation after voluntary contraction known as myotonia. Myotonia results from mis-regulated splicing of chloride channel 1 (ClC-1), leading to loss of channel function and runs of involuntary action potentials in muscle fibers. Heralding the onset of weakness, myotonia is often the first symptom of DM1, and raising the possibility that muscle hyperexcitability promotes the subsequent development of myopathy. We used genome editing to test this possibility by deleting the alternatively spliced and frameshift inducing ClC-1 exon 7a (E7a) in the Mbnl1 knockout model of DM1. Although several ClC-1 exons exhibit mis-regulated splicing in DM1, deletion of this single cryptic exon was sufficient to restore ClC-1 function and eliminate myotonia systemically and permanently. As determined by long-read sequencing, deletion of E7a reduced the frequency of other splicing defects in ClC-1 transcripts, likely as a passive consequence of restoring reading frame and nonsense surveillance. Furthermore, we observed significantly improved muscle force generation, fiber-type distribution, and histology, and partial restoration of the muscle transcriptome, including differential gene expression and alternative splicing, in non-myotonic Mbnl1 knockout mice. These results suggest that E7a inclusion is a lynchpin splice event that contributes to skeletal myopathy, highlighting myotonia as a therapeutic target and an outcome of interest in DM1.

Journal Article↗

PubMed1978

Mapping of linear and circular forms of mouse mammary tumor virus DNA with restriction endonucleases: evidence for a large specific deletion occurring at high frequency during circularization.

Rat hepatoma cells infected with mouse mammary tumor virus contain multiple forms of unintegrated viral DNA when grown in the presence of glucocorticoids. Using the DNA transfer procedure of Southern, we have prepared restriction endonuclease fragment maps of these forms of viral DNA. The maps indicate that: (i) the major species of viral DNA is a linear molecule of 5.9 X 10(6) Mr located in the cytoplasm; (ii) the nuclei contain covalently closed circular viral DNA of two distinct sizes (5.1 X 10(6) and 5.9 X 10(6) Mr) in addition to linear molecules (5.9 X 10(6) Mr); (iii) the linear molecule has specific termini; (iv) there is extensive homology between regions at or near termini of the linear molecule; (v) the predominant form of circular DNA lacks 1.2 kilobase pairs present in both the larger circular molecule and the linear molecule; and (vi) the sequences deleted from the majority of the circular DNA molecules are located at the ends of the linear DNA that are joined during circularization.

Chromosome Mapping↗

PubMed1979

New classes of viable deletion mutants in the early region of polyoma virus.

Viable mutants of polyoma virus have been isolated which have deletions in defined parts of the early region of the genome. One class of mutants has deletions (less than 1% of viral genome length) located between 71.5 and 73.5 on the physical map of polyoma virus DNA, near the origin of replication. These mutants appear to grow and to transform cells in a manner indistinguishable from wild-type virus. A second type of mutant with deletions (about 2% of viral genome length) located between about 88 and 94.5 units on the physical map of polyoma virus DNA have altered transformation properties. One of the latter (which maps between 88 and 91.5 units) also has altered growth characteristics, whereas another (which maps between 91.5 and 94.5 units) resembles wild-type virus in its growth properties. The regions with deleted sequences have been defined by cleaving mutant DNAs with restriction endonucleases and analyzing pyrimidine tracts.

Cell Transformation, Neoplastic↗

PubMed1979

Abnormal protein synthesis in malignant melanoma cells.

Abnormal proteins in neoplastic cells are present in a variety of animal tumor systems. Our laboratory has isolated several of these abnormal proteins from murine malignant melanoma by preparative gel electrophoresis; these proteins are similar in many respects to analogous proteins found in normal tissues. Examination of these proteins by polyacrylamide gel electrophoresis, amino acid analysis, carboxy and amino terminal analysis and peptide mapping after cyanogen bromide cleavage, supports the theory that these abnormal proteins are the result of deleted sequences in the peptide chain during the attempted synthesis of normal proteins in neoplastic tissue.

Amino Acids↗

PubMed1978

Further evidence for deletion of envelope glycoprotein (gp69/71) sequences in formation of Moloney-murine sarcoma virus.

Moloney-murine sarcoma virus (S+L- strain of M-MSV) has been nonproductively cloned in murine and non-murine host cells (S+L- cells) and the expression of Moloney leukaemia virus (M-MuLV) 30000 mol. wt. core protein (p30) and envelope glycoprotein (gp69/71) were studied by radioimmunoassay. Antigenic determinants of the M-MuLV p30 were associated with the sarcoma virus genome in these non-productively transformed cell clones studied, while the determinants of M-MuLV gp69/71 were not. The absence of envelope-associated glycoprotein expression in sarcoma virus transformed cells was confirmation of biological studies demonstrating that rescued sarcoma virions acquire envelope-associated properties of host range, neutralization and interference from rescuing helper virus, and further evidence that the M-MuLV gp69/71 sequences have been deleted during the formation of the M-MSV. During the course of these studies, it was also found that S+L- dog cells were releasing into culture supernatant large amounts of the p30 antigenic determinant, apparently as a soluble antigen.

Cell Line↗

PubMed2026

Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.

BACKGROUND: Gene panels represent a widely used strategy for genetic testing in a vast range of Mendelian disorders. While this approach aids reliable bioinformatic detection of short coding variants, it often fails to detect many larger variants. Recent studies have recommended the adoption of pangenome references (as opposed to linear reference genomes like GRCh38) to augment detection of large variants from targeted sequencing, potentially providing diagnostic laboratories with the possibility to streamline diagnostic work-ups and reduce costs. METHODS: Here, we analyze 1969 cardiomyopathy cases and 1805 controls sequenced with the Illumina Trusight Cardio panel using a pangenome-based workflow (GRAF) and five conventional orthogonal methodologies (GATK HaplotypeCaller, GATK-gCNV, ExomeDepth, Manta and Lumpy-SV) to detect variants ≥ 20 bp in size. RESULTS: Following lab-based variant validation by means of PCR and Sanger sequencing, we show that GRAF conjugates higher precision and recall (F1 score 0.86) compared with other methods (F1 0-0.57) in detecting potentially pathogenic variants ≥ 20 bp from short-read panel data. Results were complemented by a comparison of the tools' performance in detecting ground truth variants on reference sample HG002 from Genome In A Bottle, which confirmed GRAF to outperform other tools also on exome sequencing (F1 0.97 vs. 0-0.94). Notably, in the HG002 benchmark dataset, GRAF also showed slightly improved performance compared to GATK HaplotypeCaller in the identification of small variants (1-19 bp; F1 0.975 vs. 0.968). CONCLUSIONS: Our results indicate that pangenome-based workflows aid improved detection of large variants from targeted sequencing data in the clinical context and suggest that they may contribute to more unified variant detection frameworks for all-size genetic variants in the future.

Humans↗

PubMed1978

A single base-pair change creates a Chi recombinational hotspot in bacteriophage lambda.

X4+ mutations, responsible for the Chi phenotype in phage lambda, locally increase the rate of recombination promoted by the Escherichia coli recombination system (Rec). X+ mutations in the cII gene, one of a few sites in lambda at which such mutations arise, were located genetically and physically with overlapping deletions. DNA sequence analysis of the deletion segment containing the X+ C mutations showed that two independent X+ C mutations arose by the same A-T to T-A transversion. Presumably, this change creates a nucleotide sequence recognized by a protein involved in a rate-limiting step of recombination.

Base Sequence↗

PubMed1978

Isolation and characterization of ColE1-derived plasmid copy-number mutant.

The plasmid pBGP120 is a ColE1 derivative that contains elements of the Escherichia coli lac operon and the Tn3 transposon. We have selected and isolated a copy-number mutant of pBGP120. In exponentially growing cultures, the copy-number mutant, pOP1, represents approximately 30% of total intracellular DNA compared to about 5% for pBGP120. Plasmid-encoded beta-galactosidase monomer can represent 50% of newly synthesized protein in cells carrying pOP1. pOP1 is structurally unstable in certain genetic backgrounds and under certain growth conditions, breaking down to a smaller sized plasmid that retains the DNA overproducer phenotype and the Tn3 transposon. The smaller overproducer plasmid, pOP1delta6, is generated by a continuous deletion of sequences located between one end of the Tn3 transposon and a site about 630 nucleotides from the EcoRI site in the beta-galactosidase structural gene of pOP1. pOP1delta6 retains the ColE1 origin of replication but has lost the lac promotor and operator and most of the beta-galactosidase structural gene. pOP1delta6 exists at approximately 210 copies per chromosome in exponentially growing cells.

Bacteriocin Plasmids↗

PubMed1976

Reversion of the gal3 mutation of Escherichia coli: partial deletion of the insertion sequence.

The gal3 mutation of E. coli is an insertion of a DNA sequence, 1,100 base pairs in length, into the operator-promoter region of the galactose operon. This mutation reverts spontaneously to gal+ by excision of the insertion to produce stable, inducible revertants, or by tandem duplications of the gal operon to produce unstable, constitutive revertants. The nature of a third class of revertants, which are stable and constitutive, is the subject of the present study. The stable, constitutive class of revertants included approximately 30% of all gal+ revertants obtained from a gal3 (lambda) strain. Although the constitutive reversions could be transduced by lambda, the efficiency was found to be extremely poor and the rare transductants which did appear seemed to originate from abnormal transducing particles. It was concluded that these reversions were not normally packaged by lambda. In order to facilitate the packaging of these reversions, the chlD-pgl region was deleted from the parent gal3 (lambda) strain. Unexpectedly, the gal3 mutation in the majority of these deletions reverted to produce stable, constitutive reversions exclusively. The explanation proposed was that the chlL-pgl deletions had also removed part of the gal operator-promoter. These revertants were not considered to be true representatives of the stable, constitutive class. The specificity of deletion end-points at the insertion was found only in the gal3 (lambda) strain, and not in gal+, gal+(lambda), or gal3 strains. Moreover, the frequency of spontaneous chlD-pgl deletions increased 10- to 15-fold in presence of the gal3 insertions. A lambdagal phage bearing a true stable, constitutive reversion (galc200) was isolated from the revertant strain by subsequent deletion of the chlD-pgl segment (delta31). Electron micrographs of lambdagal+ and lambdac200 delta31(chlD pgl) DNA heteroduplexes were interpreted to indicate that the stable, constitutive reversion had arisen by a deletion of 3/4 of the gal3 insertion sequence. The main conclusions are: (i) the stable, constitutive reversions of gal3 can arise by partial deletions of the insertion sequence, apparently by elimination of the nucleotide sequence which causes polarity; (ii) the chlD-pgl deletions may exhibit preferential termination at the right extremity of the gal3 insertion in presence of prophage lambda; and (iii) the gal3 insertion appears to inhibit the production of lambdagal particles by providing a nucleotide sequence which is recognized and degraded by a specific endonuclease. It is suggested that inhibition of transducing particle formation by gal3 and the preferred termination of deletions at gal3 might represent related phenomena.

Base Sequence↗

PubMed1979

Nucleotide sequence analysis of viable deletion mutants lacking segments of the simian virus 40 genome coding for small t antigen.

The deletions in nine viable simian virus 40 mutants have been mapped by direct DNA sequence analysis. The mutant DNAs lack small segments of the early region of the viral chromosome (between 0.535 and 0.600 map unit). The deletions are all located in the region which is removed from the large T antigen transcript by splicing. No one deletion removes this entire region, but no part of this segment is conserved in all of the mutants except for several nucleotides near the splice points of the transcript. Although the deletions do not alter the region coding for the large T polypeptide, they do delete portions of the segment coding for the C-terminal half of the small t polypeptide.

Antigens, Viral↗

PubMed1978

Restriction enzyme analysis of mitochondrial DNAs of petite mutants of yeast: classification of petites, and deletion mapping of mitochondrial genes.

We have analyzed the restriction digest patterns of the mitochondrial DNA from 41 cytoplasmic petite strains of Saccharomyces cerevisiae, that have been extensively characterized with respect to genetic markers. Each mitochondrial DNA was digested with seven restriction endonucleases (EcoRI, HPaI, HindIII, BamHI, HhaI, SalI, and PstI) which together make 41 cuts in grande mitochondrial DNA and for which we have derived fragment maps. The petite mitochondrial DNAs were also analyzed with HpaII, HaeIII, and AluI, each of which makes more than 80 cleavages in grande mitochondrial DNA. On the basis of the restriction patterns observed (i.e., only one fragment migrating differently from grande for a single deletion, and more than one for multiple deletions) and by comparing petite and grande mitochondrial DNA restriction maps, the petite clones could be classified into two main groups: (1) petites representing a single deletion of grande mitochondrial DNA and (2) petites containing multiple deletions of the grande mitochondrial DNA resulting in rearranged sequences. Single deletion petites may retain a large portion of the grande mitochondrial genome or may be of low kinetic cimplexity. Many petites which are scored as single continuous deletions by genetic criteria were later demonstrated to be internally deleted by restriction endonuclease analysis. Heterogeneous sequences, manifested by the presence of sub-stoichiometric amounts of some restriction fragments, may accompany the single or multiple deletions. Single deletions with heterogeneous sequences remain useful for mapping if the low concentration sequences represent a subset of the stoichiometric bands. Using a group of petites which retain single continuous regions of the grande mitochondrial DNA, we have physically mapped antibiotic resistance and mit- markers to regions of the grande restriction map as follows: C (99.3--1.4 map units)--OXI-1 (2.5--15.7)--OXI-2 (18.5--25)--P (28.1--34.2)--OXI-3 (32.2--61.2--OII (60--62)--COB (64.6--80.8--0I (80.4--85.7)--E (95--98.9).

DNA Restriction Enzymes↗

PubMed1978

A method for detecting distant evolutionary relationships between protein or nucleic acid sequences in the presence of deletions or insertions.

A method for detecting homology between two protein or nucleic acid sequences which require insertions or deletions for optimum alignment has been devised for use with a computer. Sequences are assessed for possible relationship by Monte Carlo methods involving comparisons between the alignment of the real sequences and alignments of randomly scrambled sequences of the same composition as the real sequences, each alignment having the optimum number of gaps. As each gap is successively introduced into a comparison (real or random) a maximum score is determined from the similarity of the aligned residues. From the distribution of the maximum alignment scores of randomly scrambled sequences having the same number of gaps, the percentage of random comparisons having higher scores is determined, and the smallest of these percentage levels for each pair of sequences (real or random) indicates the optimum alignment. The fraction of the comparisons of random sequences having percentage levels at their optimum alignment below that of the real sequence comparison at its optimum estimates the probability that such an alignment might have arisen by chance. Related sequences are detected since their optimum alignment score, by virtue of a contribution from ancestral homology in addition to optimised random considerations, occupies a more extreme position in the appropriate frequency distribution of score than do the majority of optimum scores of randomly scrambled sequences in their appropriate distributions. Application of this 'optimum match' method of sequence comparison shows that the sensitivity of the 'maximum match' method of Needleman and Wunsch (1970) decreases quite dramatically with sequence comparisons which require only a few gaps for a reasonable alignment, or when sequences differ greatly in length. The 'maximum match' method as applied by Barker and Dayhoff (1972) has the additional disadvantage that deletions which have occurred in the longer of two homologous protein sequences further decrease the sensitivity of detection of relationship. The 'constrained match' method of Sankoff and Cedergren (1973) is seen to be misleading since large increments in the alignment score from added gaps do not necessarily result in a high total alignment score required to demonstrate sequence homology.

Amino Acid Sequence↗

PubMed2026

Charting host structural variations in cervical cancer by long-read sequencing pinpoints a functional deletion in PIAS1.

Host structural variations (SVs) are critical in cancer development but their landscape and interaction with HPV integration in cervical carcinogenesis remain unclear. In this study, we performed Nanopore long-read sequencing on five HPV-positive cervical cancer tissues and two cell lines to profile host SVs. We identified thousands of SVs and statistically demonstrated their significant enrichment in genomic windows ±25 to ±50 kb from HPV integration sites. Cross-sample analysis revealed 60 shared SVs, including a recurrent deletion within the PIAS1 gene. Multi-omics integration (Hi-C, H3K27ac ChIP-seq, and TCGA data) showed that this deletion is associated with reduced PIAS1 expression, disruption of local topologically associating domains, advanced pathological tumor stage, and poorer overall survival. Functional assays confirmed that PIAS1 deficiency inhibits cervical cancer cell proliferation and migration. Our findings identify a PIAS1 deletion as a candidate driver event, and underscore the pivotal role of host genomic instability in HPV-associated oncogenesis.

Cervical cancer↗

PubMed1979

Replacement of chromosome segments with altered DNA sequences constructed in vitro.

We have developed a method that may be of general application for the stable introduction of foreign sequences or deletions, constructed in vitro, into the chromosomes of Saccharomyces cerevisiae. No vector sequences are present in the final strains. Ability to transform cells with DNA, availability of a single selective marker, and integration of the transforming DNA by homologous recombination into the chromosomes are the requirements of the system. Any isolated gene can be deleted or altered and then be used to replace the wild-type chromosomal copy. An internal deletion mutant of the his3 gene and a transposition of a galactose-inducible region into chromosome XV have been generated by using the ura3 gene as the selective marker.

Chromosomes↗