High frequency targeting of genes to specific sites in the mammalian genome

We corrected a defective gene residing in the chromosome of a mammalian cell by injecting into the nucleus copies of the same gene carrying a different mutation. We determined how the number, the arrangement, and the chromosomal position of the integrated gene, as well as the number of injected molecules influence the gene-targeting frequency. Recombination between the newly introduced DNA and its chromosomal homolog occurred at a frequency of 1 in 10(3) cells receiving DNA. Correction events were mediated by either double reciprocal recombination or gene conversion. This resulted in sequences in the genome being replaced by sequences of the introduced DNA or, in separate experiments, sequences in the incoming DNA being replaced by chromosomal sequences. Both point mutations and deletion mutations were corrected; however, the nature of the mutation carried by the respective sequence influenced whether the integrated or injected sequence was corrected.     

Induction of unstable mutations in Drosophila melanogaster by microinjection of DNA from oncogenic viruses into the embryo polar plasma. II. Analysis of the role of injected DNA

We have demonstrated that the mutagenic effect of oncovirus DNA injected into Drosophila embryos is of two-type locus specificity: the spectrum of mutations induced by the retroviral cDNA (RSV) changed in different recipient stocks and those induced by the adenoviral DNA (Sa7) did not differ in the stocks studied. The Sa7 DNA and the cDNA of RSV induce mutations in different groups of loci. Transpositions of the copia element were found in mutant lines obtained in both cases.     

Genetic damage following introduction of DNA in Phycomyces

Introduction of plasmids in Phycomyces blakesleeanus caused extensive changes in the exogenous DNA and in the resident genome. Plasmids with a bacterial gene for geneticin resistance under a Phycomyces promoter were either injected into immature sporangia or incubated with spheroplasts. An improved method produced about one viable spheroplast per cell. Colonies resistant to geneticin were rare and only about 0.1% of their spores grew in the presence of geneticin. The transformation frequency was very low, < or =1 transformed colony per million spheroplasts or per microg DNA. Few nuclei in the transformants contained exogenous DNA, as shown by a selective procedure that sampled single nuclei from heterokaryons. The exogenous DNA was not integrated into the genome and no stable transformants were obtained. The plasmids were replicated in the recipient cells, but their DNA sequences were modified by deletions and rearrangements and the transformed phenotype was eventually lost. The spores developed in injected sporangia were often inviable; a genetic test showed that spore death was caused by impaired nuclear proliferation and induction of lethal mutations. About one-fourth of the viable spores from injected sporangia formed abnormal colonies with obvious changes in shape, texture, or color. The abnormalities that could be investigated were due to dominant mutations. The results indicate that incoming DNA is not only attacked, but signals a situation of stress that leads to increased mutation and nuclear and cellular death.     

Induction of unstable mutations in Drosophila melanogaster by microinjection of DNA from oncogenic viruses into the embryonic polar plasma. III. Genetic instability in the absence of an intact P-element

DNA of simian adenovirus Sa7 injected into polar plasma of early Drosophila melanogaster y1snw*; bw; st stock embryos induced one to three unstable visible X-linked mutations in the absence of intact P-element. Numerous mutational events (reversions, new mutations) occur only in four precisely destabilized by the Sa7 DNA loci of X-chromosome and take place during 4-5 generations; in the next generations the level of instability decreased. At the same time, Sa7 DNA induced reversions and new allelic mutations in the snw mutant locus, without exogenous intact P-element.     

Unstable visible mutations induced in Drosophila melanogaster by injections of oncogenic virus DNA into the polar plasm of early embryos

Summary When RSV DNA cloned in pBR 322 or DNA of simian adenovirus Sa7 (C8) is injected into the pole plasm of embryos of various Drosophila stocks, the progeny of 1–70% of the surviving flies display visible mutations. The mutagenesis is partially directed: the loci mutating due to retrovirus and adenovirus DNA do not everlap. The majority of resulting mutants are characterised by high instability: reversions and new mutations occur in them, which sometimes spread over the whole population(explosive instability). The injected sequences are revealed by dot-hybridization in the DNA of many mutant strains, but only rarely by Southern blotting procedures. The results show that the microinjection of oncovirus DNA into embryos is an approach for obtaining highly unstable strains even from wildtype stable Drosophila stocks without crosses with MR lines or the introduction of P elements. The sets of unstable mutations induced by oncovirus DNA is different from those in hybrid dysgenesis.     

Induction of unstable mutations in Drosophila melanogaster by microinjection of DNA from oncogenic viruses into the embryo polar plasma. I. Effect of the embryo genotype

We have studied the spectrum and nature of mutations induced by oncogenic virus DNA injections into wsn, T-007 line of embryos, and those of the first generation hybrids obtained after crossing the T-007 line males with the Oregon R wild line females (hybrid disgenesis). Each line is shown to have a special group of "hot" sites mutating with high frequency under the effect of the oncovirus DNA injected.     

Generation of albino Xenopus tropicalis using zinc‐finger nucleases

To generate albino lines of Xenopus tropicalis, we injected fertilized eggs with mRNAs encoding zinc‐finger nucleases (ZFNs) targeting the tyrosinase coding region. Surprisingly, vitiligo was observed on the skin of F0 frogs that had been injected with ZFN mRNAs, indicating that both tyrosinase genes in the genome were disrupted in all melanocytes within the vitiligo patches. Mutation analysis using genomic DNA from the skin revealed that two mosaic F0 frogs underwent spatially complex tyrosinase gene mutations. The data implies that the ZFN‐induced tyrosinase gene ablations occurred randomly over space and time throughout the entire body, possibly until the young tadpole stage, and that melanocyte precursors lacking functional tyrosinase proliferated and formed vitiligo patches. Several albino X. tropicalis, which are compound heterozygotes for biallelic tyrosinase mutations, were obtained by mating the mosaic F0 frogs. To our knowledge, this is the first report of the albino vertebrates generated by the targeted gene knockout.     

Bovine leukemia virus, an animal model for the study of intrastrain variability.

Intradermal injection of a cloned bovine leukemia virus (BLV) provirus (pV344) into sheep allowed direct evaluation of intrastrain variability. A sheep was injected with pV344 DNA mixed with DEAE-dextran and became persistently infected with BLV strain 344. After 18 months, DNA was extracted from peripheral blood leukocytes from a single 0.5-ml blood sample. The long terminal repeat (LTR) and the env gene were amplified by using the polymerase chain reaction, cloned, and sequenced. Nineteen independent LTR clones (0.6-kb inserts) and 16 env clones (1-kb inserts) were analyzed. The in vivo rate of nucleotide change was 0.009%/year (two mutations out of 14,464 bp in 1.5 years), corresponding to only one amino acid change in the env gene. Five point mutations (all transitions), corresponding to a modification rate of 0.034%/year (five mutations out of 9,709 bp in 1.5 years), were identified in the LTR. As a control for Taq DNA polymerase errors, the same procedure using pV344 plasmid DNA was carried out. Out of 9,944 bp sequenced, three point mutations were found (i.e., one misincorporation in 3,315 nucleotides). These data demonstrate the extremely low level (or absence) of intrastrain variability of BLV in vivo. Consequently, BLV persistence in the infected host does not seem to result from an escape mutant strategy, in sharp contrast with the high mutation rates observed in the lentivirus family. The lack of genetic variation supports the possibility of successful vaccine against BLV and probably against the related human T-cell leukemia viruses.     

Simple Methods for Generating and Detecting Locus-Specific Mutations Induced with TALENs in the Zebrafish Genome

The zebrafish is a powerful experimental system for uncovering gene function in vertebrate organisms. Nevertheless, studies in the zebrafish have been limited by the approaches available for eliminating gene function. Here we present simple and efficient methods for inducing, detecting, and recovering mutations at virtually any locus in the zebrafish. Briefly, double-strand DNA breaks are induced at a locus of interest by synthetic nucleases, called TALENs. Subsequent host repair of the DNA lesions leads to the generation of insertion and deletion mutations at the targeted locus. To detect the induced DNA sequence alterations at targeted loci, genomes are examined using High Resolution Melt Analysis, an efficient and sensitive method for detecting the presence of newly arising sequence polymorphisms. As the DNA binding specificity of a TALEN is determined by a custom designed array of DNA recognition modules, each of which interacts with a single target nucleotide, TALENs with very high target sequence specificities can be easily generated. Using freely accessible reagents and Web-based software, and a very simple cloning strategy, a TALEN that uniquely recognizes a specific pre-determined locus in the zebrafish genome can be generated within days. Here we develop and test the activity of four TALENs directed at different target genes. Using the experimental approach described here, every embryo injected with RNA encoding a TALEN will acquire targeted mutations. Multiple independently arising mutations are produced in each growing embryo, and up to 50% of the host genomes may acquire a targeted mutation. Upon reaching adulthood, approximately 90% of these animals transmit targeted mutations to their progeny. Results presented here indicate the TALENs are highly sequence-specific and produce minimal off-target effects. In all, it takes about two weeks to create a target-specific TALEN and generate growing embryos that harbor an array of germ line mutations at a pre-specified locus.     

Efficient correction of mismatched bases in plasmid heteroduplexes injected into cultured mammalian cell nuclei.

Heteroduplexes were prepared from two plasmids, pRH4-14/TK and pRH5-8/TK, containing different amber mutations in the neomycin resistance gene (Neor). The Neor gene was engineered to be expressed in both bacterial and mammalian cells. A functional Neor gene conferred kanamycin resistance to bacteria and resistance to the drug G418 to mammalian cells. In addition, the plasmids contained restriction site polymorphisms which did not confer a selectable phenotype but were used to follow the pattern of correction of mismatched bases in the heteroduplexes. In a direct comparison of the efficiency of transforming mouse LMtk- cells to G418r, the injection of heteroduplexes of pRH4-14/TK-pRH5-8/TK was 10-fold more efficient than the coinjection of pRH4-14/TK and pRH5-8/TK linear plasmid DNA. In fact, injection of 5 to 10 molecules of heteroduplex DNA per cell was as efficient in transforming LMtk- cells to G418r as the injection of 5 to 10 molecules of linear plasmid DNA per cell containing a wild-type Neor gene. To determine the pattern of mismatch repair of the injected heteroduplexes, plasmids were "rescued" from the G418r cell lines. From this analysis we conclude that the generation of wild-type Neor genes from heteroduplex DNA proceeds directly by correction of the mismatched bases, rather than by alternative mechanisms such as recombination between the injected heteroduplexes. Our finding that a cell can efficiently correct mismatched bases when confronted with preformed heteroduplexes suggests that this experimental protocol could be used to study a wide range of DNA repair mechanisms in cultured mammalian cells.     

E.coli galk和gpt基因重组质粒(pIDB103)导入金鱼受精卵内的研究

用显微注射法把含有E.coli galk和gpt基因的环状和线状重组DNApIDB103分别导入金鱼受精卵的细胞质内。这些注射过的卵子一般都能正常发育。从各不同发育时期的胚胎分离DNA与~(32)P标记的pIDB103探针杂交表明,导入的环状外源重组DNA在胚胎发育的早期,绝大部分以各种环状构型存在。从原肠胚晚期开始,它们逐渐形成串联状高分子量DNA。在尾芽期仍能检测到它们的序列。但尚未证明,它们是否与受体的染色体DNA发生整合。我们从囊胚期的胚胎中回收到了能转化大肠杆菌的环状重组DNA,它的酶切图谱和pIDB103极其相似。导入金鱼受精卵内的线状重组质粒pIDB103,除少量DNA与金鱼的染色体DNA可能发生整合外,其余绝大部分也形成高分子量DNA。     

Physical mapping of DNA-temperature-sensitive mutations of vaccinia virus

Four DNA-temperature-sensitive (ts) mutations were mapped in the genome of vaccinia virus (VV). Physical mapping of these mutations was performed by restriction analysis of the genomes of recombinants between VV DNA- ts mutants and ectromelia virus as well as by the marker rescue with cloned restriction fragments of VV DNA. One of the mutations was mapped on the HindIII-E-fragment. Biochemical studies of this mutant indicate that the mutation is not in the DNA polymerase gene which is located on the same fragment. The other three mutations were mapped in a 10 kilobase region in the middle of the HindIII-D-fragment. As shown previously, these mutations inactivate different genes, and the products of these genes participate directly in the DNA synthesis. Thus, at least three proteins involved in the VV DNA synthesis are encoded by neighboring genes in the central part of the viral genome.     

Accurate processing and amplification of cloned germ line copies of ribosomal DNA injected into developing nuclei of Tetrahymena thermophila.

The ciliate Tetrahymena thermophila contains a chromosomally integrated copy of the rRNA genes (rDNA) in its germinal (micronuclear) genome. These genes are excised from the chromosome through a process involving site-specific DNA breakage, become linear palindromic molecules with added telomeres, and are greatly amplified during development of the somatic nucleus (macronucleus). In this study, we cloned a 15-kilobase segment of the germ line DNA containing these genes and injected it into developing macronuclei of T. thermophila. Up to 11% of injected cells were transformed to the paromomycin-resistant phenotype specified by the injected DNA. Transformation efficiency was dependent on the developmental stages of the injected cells and the integrity of the injected DNA but not the DNA concentration or conformation. The injected DNA was apparently processed and amplified correctly to produce rDNA molecules with the expected linear palindromic structure which carried the appropriate physical markers. Thus, the 15-kilobase DNA contained all cis-acting sequences sufficient for the DNA-processing events leading to rDNA amplification in T. thermophila.     

Cluster of point mutations predetermined by a quasipalindromic nucleotide sequence in plasmid pBR322 DNA

Development of a cluster of point mutations due to the correction of an imperfect hairpin in plasmid DNA was investigated. Plasmid pBR322 DNA containing opposite double-strand DNA lesions in the region of a quasipalindrome was constructed. For this aim plasmid DNA was cleaved at the BamHI site, and cytosine residues of the sticky ends were modified by O-methylhydroxylamine. Modified linearized plasmid DNA was ligated and used for transformation of E.coli cells. Tetracycline-sensitive transformants were selected, and the mutants were characterized by restriction and sequencing analysis. One mutant contained a cluster of point mutations. The distribution of mutations was consistent with the cluster having arisen through correction of the imperfect hairpin formed by the quasipalindrome.