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At least 19 recordsLinked to original sources
PubMed1972

Gene selection in hemoglobin and in antibody-synthesizing cells.

Close linkage of mutually exclusive genes occurs in the non-alpha chain hemoglobin genes and in the immunoglobulin genes of man and other mammals. The expression of one gene in the cluster precludes the expression of any other linked gene. A simple, testable theory of gene selection called "looping-out excision"which was designed only to explain this mutual exclusivity in the hemoglobin system is described. The theory is closely concordant with a wide range of previously unexplained findings concerning hematopoiesis- including the developmental changes of hemoglobins, the increases in immature or fetal forms of hemoglobin that accompany anemia, and with the distribution of adult and fetal hemoglobins among erythrocytes during normal embryogenesis and in various pathological conditions. One corollary of this theory is that erythroid tissue in the normal adult bone marrow is constantly recapitulating the developmental stages of its embryogenesis. Another corollary is that the selection from among the linked globin genes occurs independently on the two chromosomes of the diploid organism. Both of these corollaries are supported by the available data. The same theory of gene selection is also remarkably consistent with known data for immunoglobulin synthesis; it could explain not only the mutually exclusive activation of linked variable genes but also the splicing which occurs between genetically linked variable and constant region genes for the immunoglobulin polypeptide chains. The agreement between these two different tissues is considered to be strong evidence that the proposed mechanism is correct at least in broad outline. Evidence from the genetics of maize and of drosophila also supports this theory of somatic tissue variegation. On the basis of these comparisons, I suggest that looping-out excision probably occurs also in other tissues and may be one means of gene selection and activation in differentiating cells.

Alleles↗
PubMed1992

Mutational spectrometry: a general approach for hot-spot point mutations in selectable genes.

To observe point mutational spectra with a high degree of precision, independent large cultures of human lymphoblastoid cells were treated with a mutagen, benzo[a]pyrene diol epoxide, and mutants at the HPRT gene were selected en masse by 6-thioguanine resistance. An average of 1.6 x 10(4) 6-thioguanine-resistant mutants were created per experiment and the kinds, positions, and numbers of the most frequent mutations were examined in exon 3 of the HPRT gene by using a high-fidelity polymerase chain reaction and denaturing gradient gel electrophoresis. Sixteen exon 3-specific mutations were found to be predominantly G----T transversions and corresponded to an average of 3500 induced mutants per experiment. Of these mutations, 6 occurred within a run of 6 guanines and 5 occurred in the sequence 5'-GAAGAG-3'. The variation among independent experiments is consistent with the numerical expectation that all 16 mutations fulfill reasonable statistical criteria for mutational hot spots. The agreement with data from various systems using clone-by-clone analysis shows that the protocol reported herein can be a useful tool to study hot-spot point mutational spectra for DNA sequences for which phenotypic selection systems exist.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1991

Gene transfer with subsequent removal of the selection gene from the host genome.

A general method of gene transfer that does not leave behind a selectable marker in the host genome is described. A luciferase gene was introduced into the tobacco genome by using the hygromycin phosphotransferase gene (hpt) as a linked selectable marker. Flanked by recombination sites from the bacteriophage P1 Cre/lox recombination system, the hpt gene was subsequently excised from the plant genome by the Cre recombinase. The Cre-catalyzed excision event in the plant genome was precise and conservative--i.e., without loss or alteration of nucleotides in the recombinant site. After removal of the Cre-encoding locus by genetic segregation, plants were obtained that had incorporated only the desired transgene. Gene transfer without the incorporation of antibiotic-resistance markers in the host genome should ease public concerns over the field release of transgenic organisms expressing such traits. Moreover, it would obviate the need for different selectable markers in subsequent rounds of gene transfer into the same host.

Agrobacterium tumefaciens↗
PubMed1988

Examination of vectors with two dominant, selectable genes for DNA repair and mutation studies in mammalian cells.

A series of vectors with two dominant selectable genes was constructed for repair and mutation studies following transfer into mammalian cells. The recombinant genes (SV-gpt and HSVtk-neo) were placed in different relative orientations and positions in the vectors. These variables were shown to affect transformation frequency of cells by the vectors especially where one of the genes had a relatively weak expression, modelled by truncating the promoter of the HSVtk-neo gene. The use of two-gene vectors to assess DNA repair was investigated by cutting the SV-gpt gene with a restriction endonuclease and monitoring correct rejoining by selecting for gene activity after transfer into various cell types. In such experiments, selection was first applied for the undamaged HSVtk-neo gene to eliminate transfer artefacts, followed by counterselection for the activity of the damaged SV-gpt gene. The measured frequency of correct rejoining of the damaged gene was found to vary both with the vector construct and with the recipient cell species (Chinese hamster V79 or human transformed fibroblasts). Despite this variation, correct rejoining was found to be consistently lower in radiosensitive (ataxia telangiectasia) human cells than in wild-type human cells, irrespective of the vector construct. In these experiments, some of the transformed cell colonies showed 'sectoring' on exposure to the counterselection, suggesting a slow determination of the fate of transferred DNA. For mutation studies a V79 cell clone carrying a single copy of one of these two-gene vectors was identified and shown to be stably integrated. Mutations of the SV-gpt gene in these cells were isolated while maintaining selection for the HSVtk-neo gene, to attempt to limit mutational loss of the total integrated sequence and provide at least one identifiable junction for analysis of deletion events. Spontaneous and X-ray-induced mutants were identified with a variety of genetic changes, as shown by Southern analysis, from presumed point mutations to deletions and rearrangements of the vector sequence. Rescue of integrated two-gene vector sequences from transformed cells, by recloning in E. coli, was shown to be feasible; thus alterations in transferred DNA can be analysed in detail.

Animals↗
PubMed1985

Differential expression of two linked selection genes (HSVI-tk and Eco.gpt) in transformed teratocarcinoma and in L cells.

Upon transfection of (TK-)F9 teratocarcinoma stem-cells and (TK-)L fibroblasts with a plasmid carrying two selection genes, Eco.gpt and HSVI-tk, selection for gpt gene yielded ten times fewer colonies than selection for tk. Only the transformed clones selected for gpt had measurable xanthine guanine phosphoribosyltransferase (XGPRT) activity (Jami et al., 1983). Eco.gpt coding for XGPRT was under the control of simian virus 40 (SV40) early genes' regulating sequences (SV-gpt). In the present study, it was verified that the low efficiency of gpt selection in mouse cells was not due to the eucaryotic controlling sequences added to the bacterial gene. The transformed clones selected for tk that had no XGPRT activity possessed at least one uninterrupted copy of the composite SV-gpt gene and as many copies of the transforming plasmid as the cells selected for gpt expression. In a further test, the gpt gene was placed under the control of tk-regulating sequences and inserted with the tk gene in the same vector. Under these conditions, expression of XGPRT in the transformed clones selected for tk was improved, even though relative selection for gpt remained low.

Animals↗
PubMed2026

Targeting DNA Methylation: New Paradigms and the Advent of Gene-Selective Tools.

DNA methylation can function as a toxic alkylation reaction exploited by chemotherapeutic agents to induce cancer cell death. However, finely tuned DNA methylation plays a fundamental role in cellular physiology, particularly in the epigenetic regulation of gene expression. Once thought to act solely as a repressor of gene transcription, its functional role has since been elucidated as genomic locus-specific and deeply connected with other epigenetic factors. Following the clinical approval of DNA methyltransferase inhibitors, such as Azacitidine and Decitabine, for the treatment of hematological malignancies, considerable efforts have been devoted to developing pharmacological tools that modulate epigenetic DNA methylation. However, the lack of gene selectivity in these agents limits their therapeutic efficacy and increases off-target toxicity. Moreover, the non-gene-selective nature of current DNA methylation-targeting molecules fails to meet the standards required to discern the nuanced roles of DNA methylation across diverse pathophysiological contexts and genomic loci, particularly in an era where next-generation sequencing and omics technologies enable high-resolution epigenetic analyses. In this review, we examine the mechanisms and roles of DNA methylation in epigenetic regulation, evaluate the current landscape of DNA methylation modulators, from traditional DNMT inhibitors to cutting-edge CRISPR-dCas9 fusion systems and protein-protein interaction disruptors, and discuss their clinical relevance. Finally, we emphasize the need for precise, locus-specific tools to advance both cancer research and therapeutic strategies.

Humans↗
PubMed1989

DNA interstrand cross-links promote chromosomal integration of a selected gene in human cells.

We have used integrative pSV2 plasmids to learn how DNA lesions affect nonhomologous recombination with human chromosomes. Enhanced stable transformation of fibrosarcoma cells with a selectable gene was observed after chemical modification of the plasmid DNA; thus, cells transfected with plasmid pSV2-gpt carrying photoadducts of the cross-linking agent 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT) yielded four- to sevenfold-higher levels of Gpt+ transformants than were obtained with untreated plasmid. The enhancement due to HMT interstrand cross-links was at least as great as that due to the monoadducts. DNA hybridization analysis indicated that the enhanced transformation frequency resulted from an increased number of cells carrying integrated plasmid sequences rather than from a higher copy number per transformant. The enhancement was not seen with a plasmid missing the sequences flanking the minimal simian virus 40 gpt transcription unit. Cotransfection with untreated and HMT-treated plasmids suggested that the HMT-containing DNA interacted preferentially with some cellular factor that promoted chromosomal integration of the plasmid DNA. It is concluded that (i) interstrand cross-linking as well as intrastrand DNA adducts promote nonhomologous recombination in human chromatin and (ii) DNA sequences flanking the selectable genes are the targets for such recombinational events.

Cell Line↗
PubMed1988

Association of high rate of recombination with amplification of dominant selectable gene in human cells.

The human cell line LM205, transformed with the pLR309 plasmid, contains a stably integrated selectable gene marker (neo) without a transcriptional promoter. Spontaneous tandem duplication at the integration site relocates a Simian virus 40 transcriptional promoter to a position 5' to the neo gene at a rate of 5 x 10(-8) events/cell/generation, as measured by subsequent resistance of the cells to the toxic antibiotic G418. The heterogeneity in the site of recombination observed in various G418-resistant (G418-R) subclones indicates that the sequences involved have little or no homology. The rate of tandem duplication involving the neo gene was not affected by DNA-damaging agents or by inhibitors of DNA synthesis. Although these tandem duplications were relatively stable in most G418-R subclones, others underwent further amplification of the neo gene during cloning. In one such cell line, RS-4, subclones isolated without G418 demonstrated a high degree of heterogeneity in the neo gene copy number (2-20), indicating that amplification was associated with a high rate of homologous recombination. Because LM205 was the only clone out of the 30 original clones transformed with pLR309 that demonstrated spontaneous G418-R colonies, cell DNA sequences near the integrated neo gene may promote this recombination. Inclusion of this cell DNA in the initial tandem duplication might then explain the high rate of duplication and deletion observed in the region of the neo gene in the RS-4 subclone.

Cell Line, Transformed↗
PubMed1988

Homologous integration in mammalian cells without target gene selection.

Homologous integrations into a nonselectable target locus have been highly enriched for following DNA transfections into mammalian cells. The target gene, the SV40 early region in COS1 cells, provides transcription signals to activate a defective selectable marker, the gpt gene. We find that nearly half of the selected clones have integrated the gpt gene at the homologous sequence in the COS1 genome. This is an estimated 100-fold enrichment for homologous events compared with transfections in which the gpt gene is transcriptionally active. As shown for yeast integration events, a double-strand break at a position of homology between the transfected DNA and the genomic target is necessary to achieve a high frequency of homologous integrations. Furthermore, the arrangement of sequences at the integration site includes a repair of the double-strand gap, which was present on the transfected DNA, suggesting that similarities exist between yeast and mammalian integrations. The experimental design, in which a defective marker is activated following a homologous integration, may have general applications for gene targeting in mammalian cells.

Animals↗
PubMed1985

Genes selectively expressed in proliferating Dictyostelium amoebae.

Few eukaryotic genes are expressed only during cell growth and division. We found that the slime mold Dictyostelium discoideum is unusual in that it expresses many genes only during proliferation. Thirty-two percent (304/950) of the sequences in a cDNA library made from vegetative mRNA were homologous to RNAs that are present at high levels during growth but at low or undetectable levels during differentiation when no cell growth occurs. In vitro translation assays confirmed that one-third of the vegetative cell mRNAs decreased in steady-state levels during differentiation. These vegetative cell-specific transcripts identified a diverse coordinately regulated class of genes: (i) 9 of the 10 cDNAs tested hybridized to unique small transcripts ranging from 400 to 620 bases long; (ii) the sequences showed various degrees of homology to related species; (iii) transcript levels synchronously fell by a factor of greater than 20 during development and synchronously increased during germination. This class of genes may play important roles in normal cell proliferation.

Cell Differentiation↗
PubMed1987

Characterization and sequence of follicle cell genes selectively expressed during vitelline membrane formation in Drosophila.

To isolate genes involved in vitelline membrane production, an ovarian cDNA library was screened with eggchamber RNAs labeled in vivo. Two cDNA clones encoding RNAs that are selectively expressed in follicle cells during the period of vitelline membrane formation were isolated. Following isolation of homologous genomic clones from a Drosophila library, one gene was localized by in situ hybridization to chromosomal region 26A, and the other to 3C. Developmental Northern blots demonstrated that both genes produce 700-800 nucleotide transcripts that accumulate during the stages of vitelline membrane synthesis. In vitro translation products from hybrid selected RNAs and DNA sequence analysis both indicate that the 26A region gene encodes a major protein component of the vitelline membrane. The structural properties of the 3C region follicle cell gene seem more compatible with an intracellular function.

Amino Acid Sequence↗
PubMed1991

A cluster of four genes selectively expressed in the male germ line of Drosophila melanogaster.

The gene Mst87F is exclusively expressed in the male germ line and is subject to translational regulation. The Mst87F mRNA is transcribed in the primary spermatocytes, stored for three days and then subsequently translated in the post-elongation period of spermiogenesis. Here we report on the isolation of a cluster of four small genes closely related in structure and function to Mst87F. These genes are located at polytene band 84D on the right arm of chromosome three and are named Mst84Da, Mst84Db, Mst84Dc and Mst84Dd. All four genes encode putative proteins composed primarily of a repetitive motif of cysteine-glycine-proline. The genes are exclusively expressed in the male germ line. The poly(A) tail of the Mst84D mRNAs increases in length at day three of pupal development, the time at which a similar change in Mst87F mRNA and translation has been shown to begin. In addition we have identified a conserved 12 base pair element within the 5' untranslated region (UTR) of each gene which is also found at an identical position in Mst87F and which has been demonstrated to be the structural element for translational control of Mst87F expression (Schäfer et al., 1990 EMBO J. 9, 4519-4525). We have mapped the gene cluster to a small deletion associated with a rotund mutation at 84D. Although flies with a homozygous deletion of the cluster still produce motile sperm, electron microscopic examination revealed numerous malformations in the ultrastructure of the axoneme resulting in a drastic reduction of motile sperm.

Amino Acid Sequence↗
PubMed1985

Replication-competent Moloney murine leukemia virus carrying a bacterial suppressor tRNA gene: selective cloning of proviral and flanking host sequences.

A bacterial suppressor tRNA gene was introduced into the long terminal repeat of the Moloney murine leukemia virus (Mo-MuLV) proviral genome to construct a retrovirus that allows easy cloning of the provirus with flanking host sequences. A replication competent virus, Mo-MuLV sup containing a tRNA amber suppressor gene, was derived that replicates to high titers in tissue culture cells and stably transduces the bacterial gene. The recombinant virus can efficiently replicate in vivo when microinjected into midgestation embryos or when injected into newborn mice and displays the same tissue tropism as wild-type Mo-MuLV. The suppressor gene in Mo-MuLV sup is functional in bacteria and allows efficient recovery of proviral genomes. This was shown by ligation of DNA from infected cells to phage lambda Charon 4A arms and selective growth of recombinant phages on su- host cells. All recovered phages contained Mo-MuLV proviral sequences and, because of the high cloning capacity of phage lambda, 1-11 kilobases of flanking host DNA. This virus should facilitate studying virus-host interactions in tissue culture cells and in animals.

Animals↗
PubMed1989

Molecular cloning of a gene selectively induced by gamma interferon from human macrophage cell line U937.

A cDNA clone encoding a gamma interferon (IFN-gamma)-inducible mRNA in human cells of the macrophage lineage was isolated and characterized. The corresponding gene, gamma.1, was selectively induced by IFN-gamma, responding a hundredfold better to IFN-gamma than to IFN-alpha. The induction was rapid and transient, with maximal mRNA accumulation at about 3 h and decline to the basal level after 48 h. Transcriptional activation could be detected as early as 5 min after IFN-gamma stimulation and accounted entirely for the mRNA accumulation. The induction of gamma.1 by IFN-gamma was cell-type restricted, being seen only in macrophages and endothelial cells. In addition, phorbol ester-induced differentiation of promyelocytic HL-60 cells and promonocytic THP-1 cells rendered the gamma.1 gene inducible by IFN-gamma. The 1.0-kilobase gamma.1 cDNA sequence encoded a small predicted polypeptide of 38 amino acids and had a conserved sequence associated with rapidly turning over mRNAs. In vitro translation of the gamma.1 transcript yielded a 4,000-dalton polypeptide.

Amino Acid Sequence↗
PubMed1992

Phenylalanine ammonia-lyase in potato (Solanum tuberosum L.). Genomic complexity, structural comparison of two selected genes and modes of expression.

Potato (Solanum tuberosum L. cv. Datura) contains approximately 40-50 phenylalanine ammonia-lyase (PAL) genes/haploid genome. Considerable cDNA heterogeneity indicates that at least about 10, and probably more, of these genes are potentially active. One subfamily, represented by one selected member (PAL-1), was analyzed with respect to genomic complexity, nucleotide and deduced amino acid sequence, and mode of constitutive or induced expression. For comparison, a second gene (PAL-2), representing several subfamilies that are easily distinguished from PAL-1, was included in these studies. Extensive structural similarities were observed both between the TATA-proximal portions of the PAL-1 and PAL-2 promoters, particularly in the areas containing putative cis-acting elements, and among all presently known PAL proteins from various higher and lower plants. The relative abundance of PAL mRNA varied greatly in several major potato organs. However, the patterns obtained with probes detecting either total PAL mRNA or more specifically, PAL-1-related or PAL-2-related mRNA species, were the same within experimental error. Mature leaves contained particularly low levels of PAL mRNA. Infection of these leaves with the pathogenic fungus, Phytophthora infestans, resulted in a large, transient induction of PAL mRNA. The relative timing of PAL-1 and PAL-2 mRNA expression, however, differed in compatible (fungus virulent, plant susceptible) but not in incompatible interactions (fungus avirulent, plant resistant). Wounding of leaves caused an extremely rapid and transient induction of both PAL mRNA species.

Amino Acid Sequence↗
PubMed1987

Selectable genes for transformation of the fungal plant pathogen Glomerella cingulata f. sp. phaseoli (Colletotrichum lindemuthianum).

Glomerella cingulata f. sp. phaseoli (Gcp) was transformed using either of two selectable markers: the amdS + gene of Aspergillus nidulans, which encodes acetamidase and permits growth on acetamide as the sole nitrogen source and the hygBR gene of Escherichia coli which encodes hygromycin B (Hy) phosphotransferase and permits growth in the presence of the antibiotic Hy. The amdS+ gene functioned in Gcp under control of A. nidulans regulatory signals and hygBR was expressed after fusion to a promoter from Cochliobolus heterostrophus, another filamentous ascomycete. Protoplasts to be transformed were generated with the digestive enzyme complex Novozym 234 and then were exposed to plasmid DNA in the presence of 10 mM CaCl2 and polyethylene glycol. Transformation occurred by integration of single or multiple copies of either the amdS+ or hygBR plasmid into the fungal genome. There was no evidence of autonomous plasmid replication. Transformants were mitotically stable on selective and nonselective media. However, transforming DNA in hygBR transformants was observed to occasionally rearrange during nonselective growth, resulting in fewer copies of the plasmid per genome. These transformants were capable of infecting bean (Phaseolus vulgaris), the Gcp host plant, and after recovery from infected tissue were found to have retained both the transforming DNA unrearranged in their genomes and the Hy resistance phenotype. All single-conidial cultures derived from both amdS+ and hygBR transformants had the transplanted phenotype, suggesting that transformants were homokaryons.

Amidohydrolases↗
PubMed1991

A dominant positive and negative selectable gene for use in mammalian cells.

We have constructed three different fusion genes containing the herpes simplex virus thymidine kinase (HSV tk) and the bacterial neomycin phosphotransferase (neo) genes. All three fusion genes utilize the HSV tk promoter but differ at the junction of their components. We have determined if the fusion genes are bifunctional by introducing them into mammalian cells and testing for function of the individual components. One of the fusion genes, TNFUS 69, produced a bicistronic message and a fusion protein that has TK and NEO protein functions. This and other fusion genes of a similar nature could serve as dominant positive and negative selectable markers in mammalian cells.

Amino Acid Sequence↗