Genetic modification technology is a new molecular tool for targeted genome modification. It includes zinc finger nucleases (ZFN) technology, transcription activator-like effector nucleases (TALEN) technology and clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) (CRISPR-Cas) nucleases technology. All of these nucleases create DNA double-strand breaks (DSB) at chromosomal targeted sites and induce cell endogenous mechanisms that are primarily repaired by the non-homologous end joining (NHEJ) or homologous recombination (HR) pathway, resulting in targeted endogenous gene knock-out or exogenous gene insertion. In recent years, genetic modification technologies have been successfully applied to bacteria, yeast, human cells, fruit fly, zebra fish, mouse, rat, livestock, cynomolgus monkey, Arabidopsis, rice, tobacco, maize, sorghum, wheat, barley and other organisms, showing its enormous advantage in gene editing field. Especially, the newly developed CRISPR-Cas9 system arose more attention because of its low cost, high effectiveness, simplicity and easiness. We reviewed the principles and the latest research progress of these three technologies, as well as prospect of future research and applications.
Animals ; CRISPR-Cas Systems ; DNA Breaks, Double-Stranded ; Endonucleases ; Genetic Engineering ; methods ; Humans ; Mutagenesis, Insertional ; Mutagenesis, Site-Directed ; Plants ; Zinc Fingers

To improve the efficiency of targeted gene replacement (TGR), a dual screen (DS) system with gusA gene as negative selective marker (GUS-DS) was developed in Magnaporthe oryzae. First, we tested the endogenous beta-glucuronidase (GUS) activities of 78 fungal strains. All tested strains were GUS-, only with 3 exceptions. Whereas, after the gusA being introduced in, M. oryzae, Fusarium oxysporum and Colletotrichum lagenarium acquired high GUS activities. The gusA is thus usable as a selective maker in fungal species. With gusA as the negative marker, HPH gene as the positive marker, and the peroxisomal targeting signal receptor genes MGPEX5 and MGPEX7 as 2 instances of target genes, we established the GUS-DS system. After transformation, we collected the transformants from hygromycin B screen media and then tested the GUS activities of them. The GUS- ones were selected as potential mutants and checked in succession by PCR and Southern blotting to identify the true mutants and calculate the efficiency of GUS-DS. As a result, GUS-DS improved the screen efficiency for delta mgpex5 from 65.8% to 90.6%, and for delta mgpex7 from 31.2% to 82.8%. In addition, we established a multiple PCR (M-PCR) method for mutant confirmation. By amplifying the different regions at the targeted locus, M-PCR differentiated the wild type, the ectopic transformants and the mutants effectively and rapidly, and had the same reliability as Southern blotting. In conclusion, GUS-DS and M-PCR are useful tools to improve the efficiency of TGR and would be helpful for fungal genomics.
Escherichia coli ; enzymology ; genetics ; Gene Expression Regulation, Enzymologic ; Genes, Fungal ; Glucuronidase ; genetics ; Magnaporthe ; genetics ; Mutagenesis, Insertional ; methods ; Mutation ; Recombination, Genetic ; Transformation, Genetic

While ica gene of Staphylococcus epidermidis is known to undergo phase variation by insertion of IS256, the phenomenon in Staphylococcus aureus has not been evaluated. Six biofilm-positive strains were tested for the presence of biofilm-nega-tive phase-variant strains by Congo red agar test. For potential phase-variant strains, pulsed-field gel electrophoresis was done to exclude the possibility of contamination. To investigate the mechanism of the biofilm-negative phase variation, PCR for each ica genes were done. Changes of ica genes detected by PCR were confirmed by southern hybridization, and their nucleotides were analyzed by DNA sequencing. Influence of ica genes and biofilm formation on capacity for adherence to biomedical material was evaluated by comparing the ability of adhering to polyurethane sur-face among a biofilm-negative phase-variant strain and its parent strain. A biofilm-negative phase-variant S. aureus strain was detected from 6 strains tested. icaC gene of the phase-variant strain was found to be inactivated by insertion of additional gene segment, IS256. The biofilm-negative phase-variant strain showed lower adher-ing capacity to polyurethane than its parent strain. This study shows that phase variation of ica gene occurs in S. aureus by insertion of IS256 also, and this biofilm-neg-ative phase variation reduces adhering capacity of the bacteria.
Bacterial Adhesion/*physiology ; Biofilms/*growth & development ; Cell Adhesion Molecules/genetics/*metabolism ; Comparative Study ; Equipment Contamination/prevention & control ; Mutagenesis, Insertional/methods ; Mutagenesis, Site-Directed/genetics ; Phase Transition ; Polysaccharides, Bacterial/genetics/*metabolism ; *Polyurethanes ; Species Specificity ; Staphylococcus aureus/cytology/*physiology ; Structure-Activity Relationship

Genetic manipulation of human pluripotent stem cells (hPSCs) provides a powerful tool for modeling diseases and developing future medicine. Recently a number of independent genome-editing techniques were developed, including plasmid, bacterial artificial chromosome, adeno-associated virus vector, zinc finger nuclease, transcription activator-like effecter nuclease, and helper-dependent adenoviral vector. Gene editing has been successfully employed in different aspects of stem cell research such as gene correction, mutation knock-in, and establishment of reporter cell lines (Raya et al., 2009; Howden et al., 2011; Li et al., 2011; Liu et al., 2011b; Papapetrou et al., 2011; Sebastiano et al., 2011; Soldner et al., 2011; Zou et al., 2011a). These techniques combined with the utility of hPSCs will significantly influence the area of regenerative medicine.
Cell Line ; Chromosomes, Artificial, Bacterial ; genetics ; Deoxyribonucleases ; genetics ; Dependovirus ; genetics ; Gene Targeting ; methods ; Genetic Engineering ; methods ; Genetic Vectors ; Genome, Human ; Humans ; Mutagenesis, Insertional ; Mutation ; Plasmids ; Pluripotent Stem Cells ; cytology ; metabolism ; Zinc Fingers ; genetics

OBJECTIVETo finish the work of sequencing the full sequence of intron 51 of dystrophin gene and understand its characteristic of sequence.

METHODSThe whole intron 51 was sequenced by primer walking. The sequencing results were analyzed by repeat sequences, matrix attachment region (MAR) and topoisomerase II cleavage sites. The residue sequences, after removal of the repetitive sequences, were subjected to the analysis of CpG islands, promoter, open reading frame (ORF) and unidentified low copy repeat sequence.

RESULTSThe acquired intron 51 sequence was composed of 38725 bp. Repetitive sequences constituted 37.53% of total intron sequence. The overall G+C content of intron 51 was 36.34%. There are four potential MARs in intron 51. Three of them are clustered in the 12 kb region near exon 51. Numerous ORFs were found on both strands, but no homologues proteins were found in Genbank CDS transcriptional peptide, PDB, SwissProt, PIR and PRF databases.

CONCLUSIONThe expansion of intron 7 over the last 120 million years was mainly the result of L1 insertion into intron 7, and not all of repetitive sequences are associated with chromosomal rearrangement. No sequence of functional significance was found in intron 51. The results suggest that the cluster of MARs may be associated with the instability of intron 51.

Base Sequence ; CpG Islands ; genetics ; Databases, Nucleic Acid ; Dystrophin ; genetics ; Gene Deletion ; Genes ; Humans ; Introns ; genetics ; Long Interspersed Nucleotide Elements ; genetics ; Mutagenesis, Insertional ; Open Reading Frames ; Promoter Regions, Genetic ; Repetitive Sequences, Nucleic Acid ; genetics ; Sequence Analysis, DNA ; methods

OBJECTIVE: To evaluate the effect of genomic instability on prognostics in nasopharyngeal carcinoma. METHODS: Genomic instability was assessed by inter-simple sequence repeats polymerase chain reaction (inter-SSR PCR) in 38 patients with nasopharyngeal carcinoma. Characterization and verification of band alterations shared in different tumors were carried out by sequencing and nest PCR. RESULTS: Thirty-one (81.6%) of the 38 patients showed genomic altercations, and genomic instability index ranged 0 to 16.2 percent. A gain-based genomic damage shared in 6 tumors was identified on chromosome 6q27. Genomic alteration was significantly more in patients less than 5-year survival than those with more than 5-year survival (P<0.05). CONCLUSION Genomic instability can be an early event marker in carcinogenesis of nasopharyngeal carcinoma. Aggravation of genomic alterations is a poor prognosis for cancer recovery.
Base Sequence ; Chromosome Deletion ; Chromosomes, Human, Pair 3 ; genetics ; Chromosomes, Human, Pair 6 ; genetics ; DNA Mutational Analysis ; Genomic Instability ; Humans ; Molecular Sequence Data ; Mutagenesis, Insertional ; Nasopharyngeal Neoplasms ; genetics ; pathology ; Polymerase Chain Reaction ; methods ; Prognosis ; Survival Analysis

The rice blast fungus Magnaporthe grisea causes one of the most destructive diseases of rice around the world. Significant progresses have been made recently in genomics studies of the fungus, opening new era of the functional genomics which requires to generate a large scale of gene knockout mutants. It has been demonstrated that T-DNA insertional mutagenesis is a powerful tool of functional genomics not only for plants but also for fungi. In this paper, we optimized the conditions for T-DNA insertional mutagenesis of M. grisea using Agrobacterium tumefaciens-mediated transformation (ATMT) approach. We employed the binary vector pBHtl constructed by Dr. S. Kang's laboratory at the Pennsylvania State University, which carries the bacterial hygromycin B phosphotransferase gene (hph) under the control of the Aspergillus nidulans trpC promoter as a selectable marker to transform the conidia of M. grisea. We optimized the conditions for T-DNA insertional mutagenesis including the medium, dosage of hygromycin B, cefotaxime and carbenicillin to select the transformants and inhibit the growth of A. tumefaciens after co-culturing. The dosage to inhibit non-transformants could vary from 200-600microg/mL among different M. grisea isolates so that the optimal dosage of the antibiotics should be decided according to isolates. Rice polished agar medium was found the best selection medium which would facilitate the mutant sporulation and minimize the contamination chance. In average, about 500 transformants could be obtained when transforming 1 x 10(6) spores at the optimum condition, among which 85% had T-DNA insertion detected by polymerase chain reaction (PCR) and thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR). Fifteen out of 1520 transformants showed mutation in colony morphology. Within 58 randomly selected mutants, it was found that there were 4 sporulation-decreased mutants, 8 less germination mutants and 9 appressorium defective mutants. Several virulent mutants to C101LAC(Pi-1)and 75-1-127(Pi-9)were also obtained which would facilitate cloning the corresponding avirulence genes.
Agrobacterium tumefaciens ; genetics ; Bacterial Proteins ; genetics ; Carbenicillin ; pharmacology ; Cefotaxime ; pharmacology ; DNA, Bacterial ; genetics ; physiology ; Genetic Vectors ; genetics ; Hygromycin B ; pharmacology ; Magnaporthe ; drug effects ; genetics ; Mutagenesis, Insertional ; methods ; Mutation ; Oryza ; microbiology ; Phosphotransferases (Alcohol Group Acceptor) ; genetics ; Polymerase Chain Reaction ; Promoter Regions, Genetic ; genetics ; Transformation, Genetic ; genetics ; physiology

Gene expression labeling and conditional manipulation of gene function are important for elaborate dissection of gene function. However, contemporary generation of pairwise dual-function knockin alleles to achieve both conditional and geno-tagging effects with a single donor has not been reported. Here we first developed a strategy based on a flipping donor named FoRe to generate conditional knockout alleles coupled with fluorescent allele-labeling through NHEJ-mediated unidirectional targeted insertion in zebrafish facilitated by the CRISPR/Cas system. We demonstrated the feasibility of this strategy at sox10 and isl1 loci, and successfully achieved Cre-induced conditional knockout of target gene function and simultaneous switch of the fluorescent reporter, allowing generation of genetic mosaics for lineage tracing. We then improved the donor design enabling efficient one-step bidirectional knockin to generate paired positive and negative conditional alleles, both tagged with two different fluorescent reporters. By introducing Cre recombinase, these alleles could be used to achieve both conditional knockout and conditional gene restoration in parallel; furthermore, differential fluorescent labeling of the positive and negative alleles enables simple, early and efficient real-time discrimination of individual live embryos bearing different genotypes prior to the emergence of morphologically visible phenotypes. We named our improved donor as Bi-FoRe and demonstrated its feasibility at the sox10 locus. Furthermore, we eliminated the undesirable bacterial backbone in the donor using minicircle DNA technology. Our system could easily be expanded for other applications or to other organisms, and coupling fluorescent labeling of gene expression and conditional manipulation of gene function will provide unique opportunities to fully reveal the power of emerging single-cell sequencing technologies.
Alleles ; Animals ; CRISPR-Cas Systems ; DNA End-Joining Repair ; DNA, Circular/metabolism* ; Embryo, Nonmammalian ; Gene Editing/methods* ; Gene Knock-In Techniques ; Gene Knockout Techniques ; Genes, Reporter ; Genetic Loci ; Genotyping Techniques ; Green Fluorescent Proteins/metabolism* ; Integrases/metabolism* ; Luminescent Proteins/metabolism* ; Mutagenesis, Insertional ; Single-Cell Analysis ; Zebrafish/metabolism*