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An active murine transposon family pair: retrotransposition of "master" MusD copies and ETn trans-mobilization.

The ETn (Early Transposon) elements are among the most active murine mobile sequences, being responsible for a series of mutations by insertion in vivo. Yet they are noncoding, and it had long been suspected that ETn are mobilized in trans by coding-competent elements, most probably from the closely related MusD family of LTR-retrotransposons. A genome-wide in silico search for coding-competent MusD elements identified a total of nine such copies, which we cloned and marked to test their transpositional activity, using an ex vivo assay in heterologous cells. Three copies were found to be autonomous for transposition, with each gag, pro, and pol MusD gene absolutely required for mobility. These active MusD copies specifically trigger retrotransposition of marked ETn elements with high efficiency, by complementation in trans. Characterization of the structures of de novo transposed MusD and ETn marked elements, as well as of their integration sites, disclosed canonical retroviral-like retrotransposition, with 6-bp target site duplications common to both elements. These results highlight the parasitic molecular strategies that are used by the ETn elements for their mobility, and unambiguously identify their "master genes."

Animals↗

Site-specific genomic integration in mammalian cells mediated by phage phiC31 integrase.

We previously established that the phage phiC31 integrase, a site-specific recombinase, mediates efficient integration in the human cell environment at attB and attP phage attachment sites on extrachromosomal vectors. We show here that phage attP sites inserted at various locations in human and mouse chromosomes serve as efficient targets for precise site-specific integration. Moreover, we characterize native "pseudo" attP sites in the human and mouse genomes that also mediate efficient integrase-mediated integration. These sites have partial sequence identity to attP. Such sites form naturally occurring targets for integration. This phage integrase-mediated reaction represents an effective site-specific integration system for higher cells and may be of value in gene therapy and other chromosome engineering strategies.

3T3 Cells↗

Genomic organization of amplified MYC genes suggests distinct mechanisms of amplification in tumorigenesis.

Integration of the human papillomavirus (HPV) genome into the host genome is associated with the disruption of the HPV E2 gene and with amplification and rearrangement of the viral and flanking cellular sequences. Molecular characterization of the genomic structures of coamplified HPV sequences and oncogenes provides essential information concerning the mechanisms of amplification and their roles in carcinogenesis. Using fluorescent hybridization on stretched DNA molecules in two cervical cancer-derived cell lines, we have elucidated the genomic structures of amplified regions containing HPV/myc genes over several hundreds of kilobases. Direct visualization of hybridization signals on individual DNA molecules suggests that overreplication and breakage-fusion-bridge-type mechanisms are involved in the genomic instability associated with HPV cervical cancers. Further analysis from two other genital cancer-derived cell lines reveals a recurrent motif of amplification, probably generated by a common mechanism involving overreplication upon viral integration. Interestingly, different amplification patterns seem to be correlated with the disease outcome, thus providing new insights into HPV-related cancer development and tumor progression.

Female↗

Integration of human papillomavirus type 16 DNA into the human genome leads to increased stability of E6 and E7 mRNAs: implications for cervical carcinogenesis.

In many cervical cancers, human papillomavirus type 16 (HPV-16) DNA genomes are found to be integrated into the host chromosome. In this study, we demonstrate that integration of HPV-16 DNA leads to increased steady-state levels of mRNAs encoding the viral oncogenes E6 and E7. This increase is shown to result, at least in part, from an increased stability of E6 and E7 mRNAs that arise specifically from those integrated viral genomes disrupted in the 3' untranslated region of the viral early region. Further, we demonstrate that the A+U-rich element within this viral early 3' untranslated region confers instability on a heterologous mRNA. We conclude that integration of HPV-16 DNA, as occurs in cervical cancers, can result in the increased expression of the viral E6 and E7 oncogenes through altered mRNA stability.

Extrachromosomal Inheritance↗

The site-specific recombination locus of mycobacteriophage Ms6 determines DNA integration at the tRNA(Ala) gene of Mycobacterium spp.

Genetic determinants of the temperate mycobacteriophage Ms6 required for chromosomal integration were identified. DNA sequence analysis of an attP-containing fragment revealed an ORF encoding a protein of 372 amino acid residues with a C-terminus similar to other conserved C-terminal regions typical of the phage integrase family. Comparison of the sequences of attP, attB and bacteria-prophage junctions attL and attR showed a 26 bp common core sequence, where recombination takes place, near the 5' end of the integrase gene. Nucleotide sequence analysis of the attB chromosomal region showed that the core site overlaps the 3' end of the tRNA(Ala) gene. An integration-proficient plasmid vector was constructed and efficiently inserted at the tRNA(Ala) gene of Mycobacterium smegmatis, Mycobacterium vaccae, Mycobacterium bovis BCG and Mycobacterium tuberculosis H37Ra. It was demonstrated that Ms6 and D29 integrative systems can be used in conjunction for inserting genes at multiple loci. The site-specific integration system of mycobacteriophage Ms6 is a new tool for mycobacterial genetic analysis and is poorly related to those of the L5 bacteriophage family.

Amino Acid Sequence↗

VGJ phi, a novel filamentous phage of Vibrio cholerae, integrates into the same chromosomal site as CTX phi.

We describe a novel filamentous phage, designated VGJ phi, isolated from strain SG25-1 of Vibrio cholerae O139, which infects all O1 (classical and El Tor) and O139 strains tested. The sequence of the 7,542 nucleotides of the phage genome reveals that VGJ phi has a distinctive region of 775 nucleotides and a conserved region with an overall genomic organization similar to that of previously characterized filamentous phages, such as CTX phi of V. cholerae and Ff phages of Escherichia coli. The conserved region carries 10 open reading frames (ORFs) coding for products homologous to previously reported peptides of other filamentous phages, and the distinctive region carries one ORF whose product is not homologous to any known peptide. VGJ phi, like other filamentous phages, uses a type IV pilus to infect V. cholerae; in this case, the pilus is the mannose-sensitive hemagglutinin. VGJ phi-infected V. cholerae overexpresses the product of one ORF of the phage (ORF112), which is similar to single-stranded DNA binding proteins of other filamentous phages. Once inside a cell, VGJ phi is able to integrate its genome into the same chromosomal attB site as CTX phi, entering into a lysogenic state. Additionally, we found an attP structure in VGJ phi, which is also conserved in several lysogenic filamentous phages from different bacterial hosts. Finally, since different filamentous phages seem to integrate into the bacterial dif locus by a general mechanism, we propose a model in which repeated integration events with different phages might have contributed to the evolution of the CTX chromosomal region in V. cholerae El Tor.

Attachment Sites, Microbiological↗

Human papillomavirus type 16 integration in cervical carcinoma in situ and in invasive cervical cancer.

Integration of human papillomavirus type 16 (HPV-16) into the host DNA has been proposed as a potential marker of cervical neoplastic progression. In this study, a quantitative real-time PCR (qRT-PCR) was used to examine the physical status of HPV-16 in 126 cervical carcinoma in situ and 92 invasive cervical cancers. Based on criteria applied to results from this qRT-PCR assay, HPV-16 was characterized in carcinoma in situ cases as episomal (61.9%), mixed (i.e., episomal and integrated; 29.4%), and integrated (8.7%) forms. In invasive cervical cancer samples, HPV-16 was similarly characterized as episomal (39.1%), mixed (45.7%), and integrated (15.2%) forms. The difference in the frequency of integrated or episomal status estimated for carcinoma in situ and invasive cervical cancer cases was statistically significant (P = 0.003). Extensive mapping analysis of HPV-16 E1 and E2 genes in 37 selected tumors demonstrated deletions in both E1 and E2 genes with the maximum number of losses (78.4%) observed within the HPV-16 E2 hinge region. Specifically, deletions within the E2 hinge region were detected most often between nucleotides (nt) 3243 and 3539. The capacity to detect low-frequency HPV-16 integration events was highly limited due to the common presence and abundance of HPV episomal forms. HPV-16 E2 expressed from intact episomes may act in trans to regulate integrated genome expression of E6 and E7.

Base Sequence↗

[Detection of integration status of human papillomavirus 16 in cervical precancerous lesions].

OBJECTIVE: To investigate the prevalence of integration of human papillomavirus 16 (HPV16) DNA into the host genome in cervical squamous intraepithelial lesions (SIL). METHODS: Multiplex PCR was used to detect the HPV/HPV16 infection and integration status of HPV16 in the surplus cells from liquid-based cytological samples from 108 patients with cervical cancer precursor lesions. Consensus primers GP5+/GP6+ were used to amplify a 150 bp long fragment in the conserved region of the HPV L1 gene so as to detect the presence pf HPV. Scion Image 4.0 electrophoresis image analysis soft was used to calculate the E2/E6 ratio so as to evaluate the episomal and integrated status of HPV16 infection: in episomal form, both targets should be equivalent, and in integrated form, E2 gene would be absent, while in mixed form of episomal/integrated mixed form, the copy number of E2 would be less than that of E6. RESULTS: Sixty-two out of the 108 patients (57.41%) had HPV infection. HPV16 were found in 32 of the 108 samples (29.63%). Among the 32 cases HPV16 DNA was exclusively episomal in 15 cases (46.88%), concomitant in 13 cases (40.62%), and integrated in 4 cases (12.50%). The prevalence of integrated and/or concomitant forms of HPV-16 DNA increased with progression of cervical disease. The prevalence of integrated form was 54.55% in the patients of CIN3 type, 50.00% in CIN2 type, 28.07% in CIN1 type, and 11.54% in the inflammatory type with significant differences between any 2 groups (all P < 0.01). CONCLUSIONS: HPV16 integration into the host genome is already present in some of CIN lesions. The multiplex PCR estimation of the HPV L1, HPV16 E2, E6 genes and E2/E6 ratio could be a simple method for detecting HPV/HPV16 infection and its integration status in liquid-based residual samples. It would be a helpful complementary tool for cytological screening to identify those patients at high risk of developing high-grade squamous intraepithelial lesions and cervical cancer.

Adult↗

Clonal origin of adenovirus type 12-induced hamster tumors: nonspecific chromosomal integration sites of viral DNA.

The mechanism of tumor induction by human adenovirus type 12 (Ad12) in newborn Syrian hamsters (Mesocricetus auratus) has been investigated further. Tumors were produced in newborn hamsters by the s.c. injection of CsCl-purified Ad12. In 60-70% of the surviving animals, tumors have been observed between 33 and 47 days after injection. In 60 independently elicited tumors, the patterns of Ad12 DNA integration have been studied by restriction enzyme analyses and Southern blot hybridization using Ad12 DNA or its terminal DNA fragments as hybridization probes. Moreover, the integrated viral genomes have been localized on different hamster chromosomes by the fluorescence in situ hybridization technique using either nonradioactively labeled digoxigenin probes and fluorescent antibodies or biotinylated probes and fluorescent avidin. In all of the tumors, 20 and more copies of viral DNA have been found covalently linked to cellular DNA, as apparent from the off-size restriction fragments that do not comigrate during electrophoreses with any of the known virion DNA fragments. In Ad12-induced tumors or Ad12-transformed hamster cell lines, there is no evidence for the persistence of nonintegrated, free viral DNA copies. In general, the multiple copies of Ad12 DNA are inserted into a single chromosomal cellular site, which is different for each tumor. Only in one tumor cell line have the integrated Ad12 DNA copies been localized on two different chromosomes. The off-size fragment patterns generated by restriction and Southern blotting experiments are also unique and different for each tumor. These off-size fragments represent the sites of linkage between viral and cellular DNA but may also contain rearranged viral DNA sequences. We conclude that, upon Ad12 tumor induction in hamsters, Ad12 DNA does not integrate at specific insertion sites or nucleotide sequences into the cellular genome. It is still possible that selective elements exist at the sites of viral DNA insertion, e.g., specific chromatin structures due to transcriptional activity. The data presented also demonstrate (a) that each tumor cell carries Ad12 DNA; (b) that the insertion site appears to be the same in each tumor cell in a given tumor; (c) that, upon continued passage of the tumor cells in culture, the chromosomal site of Ad12 DNA insertion does not change, at least up to 25-32 passages, which correspond to about 75-96 cell generations beyond the tumor stage; and (d) that the integrated Ad12 DNA is localized on different chromosomes in individual tumors. Hence, the Ad12-induced tumors are of clonal origin. Another peculiarity of this viral tumor system is the frequent occurrence of more than one tumor in one animal. By the criteria established above, each individual tumor is characterized by its specific chromosomal integration site and restriction pattern. Thus, multiple induced tumors in one animal exhibit separate and individual clonality. During the time of maximally 7 weeks of observation of Ad12-induced tumors in the animals, metastases into different organ systems have not been observed.

Adenoviruses, Human↗

Complex genomic rearrangement within the 12q15 multiple aberration region induced by integrated human papillomavirus 18 in a cervical carcinoma cell line.

Human papillomavirus (HPV) DNA is integrated into the host genome in cervical cancer. The cervical carcinoma cell line SW756 has integrated HPV-18 DNA in chromosome region 12q15, in the papillomavirus-associated locus-2 (PAL2). By polymerase chain reaction and hybridization of an arrayed cosmid library with oligonucleotides from the rearranged allele, we determined the pre-integration germline structure of the region. PAL2 was located approximately 10 kb from sequence-tagged site marker U27131, which was the marker most proximal to the 3' flank of the integrated viral DNA. HPV-18 DNA integration induced a complex genomic rearrangement resulting in inversion and deletion of cellular sequences. PAL2 is within the multiple aberration region, which has been shown to be affected in several types of benign tumors of mesenchymal origin. The integrated viral DNA was located 50 kb from a CpG island and 150 kb upstream of the high-mobility group I-C (HMGI-C) gene. The HMGI-C gene and the integrated HPV-18 DNA had opposite transcriptional orientations. No overexpression or altered message of the HMGI-C gene was detected in three cervical carcinoma cell lines. The integrated viral DNA did not affect any other known gene in the region and may be a marker for an unknown gene associated with malignant tumor phenotypes.

Base Sequence↗

Detection of human papillomavirus type 16 integration in pre-neoplastic cervical lesions and confirmation by DIPS-PCR and sequencing.

BACKGROUND: Persistent infections with high-risk types of human papillomavirus (HR-HPV) favour integration of viral DNA into the host cells and are associated with cervical carcinoma. HPV16 is the prevalent HR-type worldwide associated to cervical cancer. Integration of viral DNA promotes a selective cell growth advantage, resulting a risk factor for cancer development. OBJECTIVES: To test physical status of HPV16 infection in pre-neoplastic cervical lesions using a quantitative real time-PCR (QRT-PCR) based method. To investigate reliability of this method in identification of HPV16 integrated sequences, by detection of integrated papillomavirus sequences (DIPS-PCR) assay and sequencing. STUDY DESIGN: One hundred and seventy HR-HPV positive archival cervical specimens were tested for presence of HPV16 DNA. In HPV16 positive samples, viral load and physical status were evaluated. RESULTS: HPV16 DNA was detected in 74/170 (43%) HR-HPV positive specimens. In 52/74 a QRT-PCR was performed, and 3 integrated, 13 mixed and 36 episomal forms were detected. Presence of integrated forms was confirmed by DIPS-PCR and sequencing. CONCLUSIONS: Presence of HPV integrated forms was detected and confirmed in pre-neoplastic cervical lesions. The QRT-PCR method we used is sensitive and specific for identification of HPV integration in cervical samples, and may be suitable for large scale investigations with prognostic and clinical implications in management of cervical cancer.

Base Sequence↗

Complete genomic sequence of the temperate bacteriophage PhiAT3 isolated from Lactobacillus casei ATCC 393.

The complete genomic sequence of a temperate bacteriophage PhiAT3 isolated from Lactobacillus (Lb.) casei ATCC 393 is reported. The phage consists of a linear DNA genome of 39,166 bp, an isometric head of 53 nm in diameter, and a flexible, noncontractile tail of approximately 200 nm in length. The number of potential open reading frames on the phage genome is 53. There are 15 unpaired nucleotides at both 5' ends of the PhiAT3 genome, indicating that the phage uses a cos-site for DNA packaging. The PhiAT3 genome was grouped into five distinct functional clusters: DNA packaging, morphogenesis, lysis, lysogenic/lytic switch, and replication. The amino acid sequences at the NH2-termini of some major proteins were determined. An in vivo integration assay for the PhiAT3 integrase (Int) protein in several lactobacilli was conducted by constructing an integration vector including PhiAT3 int and the attP (int-attP) region. It was found that PhiAT3 integrated at the tRNAArg gene locus of Lactobacillus rhamnosus HN 001, similar to that observed in its native host, Lb. casei ATCC 393.

Bacteriophages↗

Similarities between initiation of V(D)J recombination and retroviral integration.

In the first step of V(D)J recombination, the RAG1 and RAG2 proteins cleave DNA between a signal sequence and the adjacent coding sequence, generating a blunt signal end and a coding end with a closed hairpin structure. These hairpins are intermediates leading to the formation of assembled antigen receptor genes. It is shown here that the hairpins are formed by a chemical mechanism of direct trans-esterification, very similar to the early steps of transpositional recombination and retroviral integration. A minor variation in the reaction is sufficient to divert the process from transposition to hairpin formation.

Base Sequence↗

Human-specific integrations of the HERV-K endogenous retrovirus family.

Several distinct families of endogenous retrovirus-like sequences (HERVs) exist in the genomes of humans and other primates. One of these families, the HERV-K group, contains members that encode functional proteins and that have been implicated in the etiology of insulin-dependent diabetes mellitus (IDDM). Because of potential functional and disease relevance, it is important to determine if there are HERV-K-associated genetic differences between individuals. In this study, we have investigated the divergence and evolutionary age of HERV-K long terminal repeats (LTRs). Thirty-seven LTRs, taken primarily from random human clones in GenBank, were aligned and grouped into nine clusters with decreasing sequence divergence. Cluster 1 sequences are 8.6% divergent, on average, whereas cluster 9 LTRs, represented by the LTRs of the fully sequenced HERV-K10 clone, show an average of only 1.1% divergence from each other. The evolutionary age of 18 LTRs from different clusters was then investigated by genomic PCR to determine presence or absence of the retroviral element in different primate species. LTRs from clusters of higher divergence were detected in monkeys and apes, whereas LTRs in clusters with lower divergence were acquired later in evolution. Notably, LTRs of cluster 9 were found only in humans at all nine loci examined. Genomic Southern analysis with an oligonucleotide probe specific for cluster 9 LTRs suggests that HERV-K elements with this type of LTR expanded independently in the genomes of humans and the great apes. This is the first report of endogenous retroviral integrations that are specific to humans and indicates that some HERVs have amplified much later than previously thought. These elements may still be actively transposing and may therefore represent a source of genetic variation linked to disease development.

Animals↗

Site-specific transformation of Drosophila via phiC31 integrase-mediated cassette exchange.

Position effects can complicate transgene analyses. This is especially true when comparing transgenes that have inserted randomly into different genomic positions and are therefore subject to varying position effects. Here, we introduce a method for the precise targeting of transgenic constructs to predetermined genomic sites in Drosophila using the C31 integrase system in conjunction with recombinase-mediated cassette exchange (RMCE). We demonstrate the feasibility of this system using two donor cassettes, one carrying the yellow gene and the other carrying GFP. At all four genomic sites tested, we observed exchange of donor cassettes with an integrated target cassette carrying the mini-white gene. Furthermore, because RMCE-mediated integration of the donor cassette is necessarily accompanied by loss of the target cassette, we were able to identify integrants simply by the loss of mini-white eye color. Importantly, this feature of the technology will permit integration of unmarked constructs into Drosophila, even those lacking functional genes. Thus, C31 integrase-mediated RMCE should greatly facilitate transgene analysis as well as permit new experimental designs.

Animals↗

High frequency expression of integrated proviruses derived from enhancer trap retroviruses.

Since retroviruses integrate preferentially into transcriptionally active loci, the provirus may come under the control of regulatory elements of the gene into which it integrated and thus become a functional tag for that gene. In order to determine the frequency of retroviral integration near active endogenous enhancer elements, a retroviral enhancer trap vector was constructed. Lacking the long terminal repeat enhancer, expression of the neomycin resistance (neo) gene, used as a reporter, is dependent upon endogenous enhancer elements able to activate the long terminal repeat promoter. Infection of murine fibroblast cells indicated that a high proportion of the proviral copies expressed the neo gene. Infection of hematopoietic lines confirmed this high frequency of expression of integrated proviruses. Overall, between 43 and 74% of proviruses integrated into several different cell lines expressed the neo gene. These data suggest that retroviral integration is not only dependent upon transcriptional activity of the genomic target sites, but, more specifically, retroviruses preferentially integrate near active enhancer elements which are often associated with developmentally regulated genes.

3T3 Cells↗

Identification of the second attachment site for HP1 and S2 bacteriophages in Haemophilus influenzae genome.

Presented data demonstrate that both HP1c1 and S2 bacteriophages of Haemophilus influenzae can use two related attB sites on the host chromosome. The first indication comes from the analysis of the whole genome sequence of H. influenzae Rd in which a second region of nucleotide sequence identical with the known attB site was detected. The location of both attB sites agrees with results of earlier field-inversion gel electrophoresis (FIGE) analysis of S2 and HP1c1 lysogens of H. influenzae. Functionality of cloned attB sites in the integration process of both phages was confirmed using in vivo integrase-dependent recombination system in Escherichia coli. Presented results seem to extend previously described similarities between S2 and HP1c1 phages.

Attachment Sites, Microbiological↗

Molecular analysis of cellular loci disrupted by papillomavirus 16 integration in cervical cancer: frequent viral integration in topologically destabilized and transcriptionally active chromosomal regions.

To discern the structural features of cellular loci that are disrupted by type 16 human papillomavirus (HPV-16) integration in cervical cancer, a polymerase chain reaction (PCR)-based strategy was employed for direct amplification and sequence analysis of four such cellular loci in cancer biopsy samples. One of the HPV-16-disrupted loci was found to be the microtubule-associated protein (MAP-2) gene and the other three loci were uncharacterized and were designated PID-1 to -3 (for papillomavirus integration-disrupted). The junctional sequences of the viral integration sites in the four loci analyzed are bracketed by long tracts of homogeneous purine or pyrimidine or alternating purine-pyrimidine which are known to destabilize the B-form conformation of the DNA structure. Using a panel of human/hamster hybrid cell DNAs and PCR analysis, the four loci were assigned to chromosomes 2 (MAP-2), 9 (PID-1), 1 (PID-2) and 8 (PID-3), respectively. These chromosomes carry numerous other previously determined viral integration and chromosomal fragile sites and the myc oncogenes. The PID-1 locus was further found in Southern analysis to be rearranged and amplified in another cervical cancer biopsy and a cervical carcinoma cell line (CaSki). On Northern analysis, the PID-1 and -3 probes detected a 3.0- and a 3.6-kb transcript, respectively, in normal cervical cells and in cervical cancer cell lines. The findings suggest that HPV-16 genome integrates frequently into topologically destabilized and transcriptionally active chromosomal sites. It remains to be elucidated whether the MAP-2 and the PID loci contribute to the pathogenesis of cervical cancer.

Base Sequence↗