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International Journal of Molecular... Aug 2021species transfer DNA (T-DNA) to plant cells where it may integrate into plant chromosomes. The process of integration is thought to involve invasion and ligation of... (Review)
Review
species transfer DNA (T-DNA) to plant cells where it may integrate into plant chromosomes. The process of integration is thought to involve invasion and ligation of T-DNA, or its copying, into nicks or breaks in the host genome. Integrated T-DNA often contains, at its junctions with plant DNA, deletions of T-DNA or plant DNA, filler DNA, and/or microhomology between T-DNA and plant DNA pre-integration sites. T-DNA integration is also often associated with major plant genome rearrangements, including inversions and translocations. These characteristics are similar to those often found after repair of DNA breaks, and thus DNA repair mechanisms have frequently been invoked to explain the mechanism of T-DNA integration. However, the involvement of specific plant DNA repair proteins and proteins in integration remains controversial, with numerous contradictory results reported in the literature. In this review I discuss this literature and comment on many of these studies. I conclude that either multiple known DNA repair pathways can be used for integration, or that some yet unknown pathway must exist to facilitate T-DNA integration into the plant genome.
Topics: Agrobacterium; Chromosomes, Plant; DNA Repair; DNA, Bacterial; DNA, Plant; Plants; Transformation, Genetic
PubMed: 34445162
DOI: 10.3390/ijms22168458 -
Communications Biology Jul 2023Hepatitis B virus (HBV) may integrate into the genome of infected cells and contribute to hepatocarcinogenesis. However, the role of HBV integration in hepatocellular...
Hepatitis B virus (HBV) may integrate into the genome of infected cells and contribute to hepatocarcinogenesis. However, the role of HBV integration in hepatocellular carcinoma (HCC) development remains unclear. In this study, we apply a high-throughput HBV integration sequencing approach that allows sensitive identification of HBV integration sites and enumeration of integration clones. We identify 3339 HBV integration sites in paired tumour and non-tumour tissue samples from 7 patients with HCC. We detect 2107 clonally expanded integrations (1817 in tumour and 290 in non-tumour tissues), and a significant enrichment of clonal HBV integrations in mitochondrial DNA (mtDNA) preferentially occurring in the oxidative phosphorylation genes (OXPHOS) and D-loop region. We also find that HBV RNA sequences are imported into the mitochondria of hepatoma cells with the involvement of polynucleotide phosphorylase (PNPASE), and that HBV RNA might have a role in the process of HBV integration into mtDNA. Our results suggest a potential mechanism by which HBV integration may contribute to HCC development.
Topics: Humans; Hepatitis B virus; Carcinoma, Hepatocellular; Liver Neoplasms; DNA, Mitochondrial; Virus Integration; Mitochondria
PubMed: 37400627
DOI: 10.1038/s42003-023-05017-4 -
Bioscience Reports Jan 2021CRISPR systems build adaptive immunity against mobile genetic elements by DNA capture and integration catalysed by Cas1-Cas2 protein complexes. Recent studies suggested...
CRISPR systems build adaptive immunity against mobile genetic elements by DNA capture and integration catalysed by Cas1-Cas2 protein complexes. Recent studies suggested that CRISPR repeats and adaptation module originated from a novel type of DNA transposons called casposons. Casposons encode a Cas1 homologue called casposase that alone integrates into target molecules single and double-stranded DNA containing terminal inverted repeats (TIRs) from casposons. A recent study showed Methanosarcina mazei casposase is able to integrate random DNA oligonucleotides, followed up in this work using Acidoprofundum boonei casposase, from which we also observe promiscuous substrate integration. Here we first show that the substrate flexibility of Acidoprofundum boonei casposase extends to random integration of DNA without TIRs, including integration of a functional gene. We then used this to investigate targeting of the casposase-catalysed DNA integration reactions to specific DNA sites that would allow insertion of defined DNA payloads. Casposase-Cas9 fusions were engineered that were catalytically proficient in vitro and generated RNA-guided DNA integration products from short synthetic DNA or a gene, with or without TIRs. However, DNA integration could still occur unguided due to the competing background activity of the casposase moiety. Expression of Casposase-dCas9 in Escherichia coli cells effectively targeted chromosomal and plasmid lacZ revealed by reduced β-galactosidase activity but DNA integration was not detected. The promiscuous substrate integration properties of casposases make them potential DNA insertion tools. The Casposase-dCas9 fusion protein may serves as a prototype for development in genetic editing for DNA insertion that is independent of homology-directed DNA repair.
Topics: CRISPR-Cas Systems; DNA; DNA Transposable Elements; Escherichia coli; In Vitro Techniques; Methanosarcina; R-Loop Structures; Substrate Specificity
PubMed: 33289517
DOI: 10.1042/BSR20203595 -
The CRISPR Journal Oct 2022While genome editing has been revolutionized by the advent of CRISPR-based nucleases, difficulties in achieving efficient, nuclease-mediated, homology-directed repair...
While genome editing has been revolutionized by the advent of CRISPR-based nucleases, difficulties in achieving efficient, nuclease-mediated, homology-directed repair (HDR) still limit many applications. Commonly used DNA donors such as plasmids suffer from low HDR efficiencies in many cell types, as well as integration at unintended sites. In contrast, single-stranded DNA (ssDNA) donors can produce efficient HDR with minimal off-target integration. In this study, we describe the use of ssDNA phage to efficiently and inexpensively produce long circular ssDNA (cssDNA) donors. These cssDNA donors serve as efficient HDR templates when used with Cas9 or Cas12a, with integration frequencies superior to linear ssDNA (lssDNA) donors. To evaluate the relative efficiencies of imprecise and precise repair for a suite of different Cas9 or Cas12a nucleases, we have developed a modified traffic light reporter (TLR) system (TLR-multi-Cas variant 1 [MCV1]) that permits side-by-side comparisons of different nuclease systems. We used this system to assess editing and HDR efficiencies of different nuclease platforms with distinct DNA donor types. We then extended the analysis of DNA donor types to evaluate efficiencies of fluorescent tag knockins at endogenous sites in HEK293T and K562 cells. Our results show that cssDNA templates produce efficient and robust insertion of reporter tags. Targeting efficiency is high, allowing production of biallelic integrants using cssDNA donors. cssDNA donors also outcompete lssDNA donors in template-driven repair at the target site. These data demonstrate that circular donors provide an efficient, cost-effective method to achieve knockins in mammalian cell lines.
Topics: Humans; CRISPR-Cas Systems; DNA; DNA, Single-Stranded; Endonucleases; Gene Editing; HEK293 Cells; K562 Cells
PubMed: 36070530
DOI: 10.1089/crispr.2022.0058 -
Frontiers in Cellular and Infection... 2022The incidence of cancer is high worldwide, and biological factors such as viruses and bacteria play an important role in the occurrence of cancer. , , and other... (Review)
Review
The incidence of cancer is high worldwide, and biological factors such as viruses and bacteria play an important role in the occurrence of cancer. , , and other organisms have been identified as carcinogens. Cancer is a disease driven by the accumulation of genome changes. Viruses can directly cause cancer by changing the genetic composition of the human body, such as cervical cancer caused by DNA integration and liver cancer caused by DNA integration. Recently, bacterial DNA has been found around cancers such as pancreatic cancer, breast cancer and colorectal cancer, and the idea that bacterial genes can also be integrated into the human genome has become a hot topic. In the present paper, we reviewed the latest phenomenon and specific integration mechanism of bacterial DNA into the human genome. Based on these findings, we also suggest three sources of bacterial DNA in cancers: bacterial DNA around human tissues, free bacterial DNA in bacteremia or sepsis, and endogenous bacterial DNA in the human genome. Clarifying the theory that bacterial DNA integrates into the human genome can provide a new perspective for cancer prevention and treatment.
Topics: Female; Humans; DNA, Bacterial; Virus Integration; Carcinogenesis; Uterine Cervical Neoplasms; Genome, Human; DNA, Viral
PubMed: 36310856
DOI: 10.3389/fcimb.2022.996778 -
Annals of the New York Academy of... Nov 1995Studies have been designed to examine the potential integration of DNA vaccines into the host cell genome. This is of concern because of the possibility of insertional... (Review)
Review
Studies have been designed to examine the potential integration of DNA vaccines into the host cell genome. This is of concern because of the possibility of insertional mutagenesis resulting in the inactivation of tumor suppressor genes or the activation of oncogenes. The requirements for adequate testing were determined to be (1) a method to purify host cell genomic DNA from nonintegrated free plasmid, (2) a sensitive method to detect integrated plasmid in the purified genomic DNA, and (3) stringent methods to avoid contamination. These requirements were fulfilled by agarose-gel electrophoresis, the polymerase chain reaction, and separation of each activity with stringent handling procedures, respectively. An exploratory experiment was carried out in which mice were injected with 100 micrograms of vaccine plasmid DNA in each quadriceps. Examination of quadriceps and 12 other tissues at several time points failed to reveal any evidence of integration at a sensitivity level that could detect 1 to 7.5 integrations in 150,000 nuclei. A worst-case scenario determined that this would be at least 3 orders of magnitude below the spontaneous mutation frequency.
Topics: Animals; DNA, Recombinant; Genes, Viral; Influenza A virus; Influenza Vaccines; Mice; Mice, Inbred BALB C; Nucleocapsid Proteins; Nucleoproteins; Organ Specificity; Plasmids; Polymerase Chain Reaction; RNA-Binding Proteins; Recombinant Fusion Proteins; Risk Assessment; Safety; Sensitivity and Specificity; Tissue Distribution; Vaccination; Vaccines, Synthetic; Viral Core Proteins; Viral Structural Proteins; Virus Integration
PubMed: 8546411
DOI: 10.1111/j.1749-6632.1995.tb44729.x -
Molecular Biology & Medicine Jun 1990Hepatitis B virus (HBV) DNA integrates into human hepatocyte DNA. We have gathered the available data on the structure of the integrants from human hepatocellular... (Review)
Review
Hepatitis B virus (HBV) DNA integrates into human hepatocyte DNA. We have gathered the available data on the structure of the integrants from human hepatocellular carcinomas, and classified them into those that seem to represent primary integrants and those that are the products of secondary rearrangements. By means of structural analyses of the possible primary integrants, we deduced that the replication intermediates of the viral genome are the preferred substrates for integration. The integrated HBV DNA and the target cellular DNA are invariably associated with deletions, possibly reflecting the substrate for, and the mechanism of, the integration reaction. The target cell DNA sequence, as well as the target site of integration in chromosomes, seems to be selected randomly, suggesting that HBV DNA integration should bring about random mutagenic effects. Several samples recovered from hepatocellular carcinomas show that the integrated HBV DNA can mediate secondary rearrangements of chromosomes, such as translocations, inversions, deletions and (possibly) amplifications. Thus, HBV DNA integration causes multiple mutagenic effects. We argue that during hepatitis infection, the tendency of rearrangement of hepatocyte chromosomes is combined with the forcible turnover of cells. This is a constantly operating system for the selection of cells that grow better than average cells, possibly involving important steps in multistaged hepatocarcinogeneses.
Topics: Carcinoma, Hepatocellular; Cell Division; Chromosome Aberrations; Chromosome Deletion; Chromosome Mapping; DNA, Neoplasm; DNA, Viral; Gene Expression Regulation, Neoplastic; Gene Expression Regulation, Viral; Genes, Viral; Hepatitis B; Hepatitis B virus; Humans; Liver Neoplasms; Liver Regeneration; Mutation; Recombination, Genetic; Virus Replication
PubMed: 2170810
DOI: No ID Found -
The Plant Journal : For Cell and... Aug 2022High efficiency site-directed chromosomal integration of exogenous DNA in plants remains a challenge despite recent advances in genome editing technologies. One approach...
High efficiency site-directed chromosomal integration of exogenous DNA in plants remains a challenge despite recent advances in genome editing technologies. One approach to mitigate this problem is to increase the effective concentration of the donor DNA at the target site of interest. HUH endonucleases (ENs) coordinate rolling circle replication. In vitro, they can form stable covalent bonds with DNA that carries their recognition motifs. When fused to a CRISPR-associated endonuclease, HUH ENs may improve integration rates by increasing the local donor concentration through tethering of the donor to the CRISPR nuclease. We tested this hypothesis by using chimeric proteins between LbCas12a as a CRISPR-associated endonuclease and the HUH EN from Faba Bean Necrotic Yellow Virus in soybean (Glycine max). Two fusion protein configurations were tested to integrate a 70-nt oligonucleotide donor into a commercially important target site using protoplasts and in planta transformation. Site-directed integration rates of the donor DNA, when tethered to the fusion protein, reached about 26% in plants and were up to four-fold higher than in untethered controls. Integrations via canonical homology-directed repair or non-homologous end joining were promoted by tethering in a similar fashion. This study is the first demonstration of HUH EN-associated tethering to improve site-directed DNA integration in plants.
Topics: CRISPR-Cas Systems; DNA; Endonucleases; Gene Editing; Genome, Plant; Glycine max
PubMed: 35635764
DOI: 10.1111/tpj.15849 -
Gene Therapy Jun 2022While generally referred to as "non-integrating" vectors, adenovirus vectors have the potential to integrate into host DNA via random, illegitimate (nonhomologous)...
While generally referred to as "non-integrating" vectors, adenovirus vectors have the potential to integrate into host DNA via random, illegitimate (nonhomologous) recombination. The present study provides a quantitative assessment of the potential integration frequency of adenovirus 5 (Ad5)-based vectors following intravenous injection in mice, a common route of administration in gene therapy applications particularly for transgene expression in liver. We examined the uptake level and persistence in liver of first generation (FG) and helper-dependent (HD) Ad5 vectors containing the mouse leptin transgene. As expected, the persistence of the HD vector was markedly higher than that of the FG vector. For both vectors, the majority of the vector DNA remained extrachromosomal and predominantly in the form of episomal monomers. However, using a quantitative gel-purification-based integration assay, a portion of the detectable vector was found to be associated with high molecular weight (HMW) genomic DNA, indicating potential integration with a frequency of up to ~44 and 7000 integration events per μg cellular genomic DNA (or ~0.0003 and 0.05 integrations per cell, respectively) for the FG and HD Ad5 vectors, respectively, following intravenous injection of 1 × 10 virus particles. To confirm integration occurred (versus residual episomal vector DNA co-purifying with genomic DNA), we characterized nine independent integration events using Repeat-Anchored Integration Capture (RAIC) PCR. Sequencing of the insertion sites suggests that both of the vectors integrate randomly, but within short segments of homology between the vector breakpoint and the insertion site. Eight of the nine integrations were in intergenic DNA and one was within an intron. These findings represent the first quantitative assessment and characterization of Ad5 vector integration following intravenous administration in vivo in wild-type mice.
Topics: Adenoviridae; Animals; DNA; Genetic Vectors; Genomics; Injections, Intravenous; Liver; Mice
PubMed: 34404916
DOI: 10.1038/s41434-021-00278-2 -
Cell Stem Cell Oct 2022Therapeutic gene editing based on homology-directed repair (HDR) promises to precisely recombine donor template sequences at programmed double-strand break sites. In...
Therapeutic gene editing based on homology-directed repair (HDR) promises to precisely recombine donor template sequences at programmed double-strand break sites. In this issue, Ferrari et al. report that commonly used AAV donors blunt hematopoietic repopulation and result in frequent genomic integrations that could interfere with normal gene expression.
Topics: CRISPR-Cas Systems; DNA; DNA Breaks, Double-Stranded; DNA End-Joining Repair; Gene Editing; Hematopoietic Stem Cells; Recombinational DNA Repair
PubMed: 36206729
DOI: 10.1016/j.stem.2022.09.003