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Genetic reshuffling reconstitutes functional expression cassettes in retroviral vectors.

BACKGROUND: A major prerequisite for the design of retroviral vectors encoding cell toxic or harmful genes is the possibility to tightly control gene expression, thus limiting activity to the relevant target cells and protecting the packaging cell used for production of recombinant viral particles. METHODS: In the present study a system was developed in which genetic reshuffling during the retroviral life cycle is exploited, allowing reconstitution of functional expression cassettes from separate elements exclusively in transduced target cells. For construction of these murine leukaemia virus (MLV)-based reconstituting viral vectors (ReCon), a promoterless inverted enhanced green fluorescent protein (EGFP) reporter gene cassette was inserted in place of the U3 region of the 3' LTR. Subsequently, the human ubiquitin promoter was inserted in the inverse orientation into the R/U5 border of the 5' LTR of the vector. RESULTS: PA317 packaging cells stably transfected with ReCon vectors were established and EGFP expression was analysed by fluorescence-activated cell sorting (FACS). After detection of low-level background expression, an additional polyadenylation signal was introduced in antisense orientation into the 3' LTR at the R/U5 border to prevent accidental read-through transcription from neighbouring cellular promoters. Virus-containing cell culture supernatants were then used to infect NIH3T3 target cells. EGFP expression, recloning and sequencing of integrated proviruses demonstrated the correct reassembly of the transduced ubiquitin/EGFP transcription unit in these infected cells. CONCLUSIONS: This facile and convenient system should allow production of retroviral vectors encoding potentially toxic proteins, cell cycle inhibitors or inducers of apoptosis, all of which would interfere with vector production if expressed in the retroviral packaging cell.

3T3 Cells↗

Molecular evidence of HTLV-1 intrafamilial transmission in a non-endemic area in Argentina.

In the North of Argentina, an endemic area for HTLV-1, intrafamilial transmission of this virus has been observed. The HTLV-1 status in 13 family members of a seropositive blood donor from the central region of Argentina (non-endemic area) was investigated. According to serological and molecular assays, four members of this family (the blood donor, the husband, a son, and a daughter-in-law) proved to be HTLV-1 positive. LTR, tax, and env sequences from the provirus infecting the family members were identical. This strongly suggests the intrafamilial transmission of the virus. This study demonstrated intrafamilial transmission of HTLV-1 in a non-endemic area of Argentina.

Adult↗

Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex.

The Saccharomyces sensu stricto complex consists of six closely related species and one natural hybrid. Intra- and inter- species variability in repetitive elements can help elucidate the population structure and evolution of these close relatives. The chromosome positions of several telomeric associated sequences (TASs) and LTR-retrotransposons have been determined, using PFGE, in 112 isolates. Most of the repetitive elements studied are found in multiple copies in each strain, although in some subpopulations these elements are present in low copy number or are absent. Hybridization patterns and copy numbers of the repetitive elements correlate with geographic distribution. These patterns may yield interesting clues as to the origins and evolution of some TASs and retrotransposons, e.g. we can infer that Y' originated on the left end of chromosome XIV. There is strong evidence for horizontal transfer of Ty2 between S. cerevisiae and S. mikatae. Ty1 and Ty5 are either lost easily or frequently horizontally transferred. We have also found some gross chromosomal rearrangements in isolates within species and a few new natural hybrids between species, indicating that these processes occur in the wild and are not limited to conditions of human influence. DNA sequences have been deposited with the EMBL/GenBank database under Accession Nos AJ632279-AJ632293.

Base Sequence↗

The diversity of retrotransposons in the yeast Cryptococcus neoformans.

We have undertaken an analysis of the retrotransposons in the medically important basidiomycetous fungus Cryptococcus neoformans. Using the data generated by a C. neoformans genome sequencing project at the Stanford Genome Technology Center, 15 distinct families of LTR retrotransposons and several families of non-LTR retrotransposons were identified. Members of at least seven families have transposed recently and are probably still active. For several families, only partial elements could be identified and these are quite diverse in sequence, suggesting that they are ancient components of the C. neoformans genome. Most C. neoformans elements are not closely related to previously identified fungal retrotransposons, suggesting that the diversity of fungal retrotransposons has been only sparsely sampled to date. C. neoformans has fewer distinct retrotransposon families than Candida albicans (37 or more), in particular fewer families represented solely by ancient and inactive elements, but it has considerably more families than either Saccharomyces cerevisiae (five) or Schizosaccharomyces pombe (two). The findings suggest that elimination of retrotransposons is faster in C. neoformans than in C. albicans, but perhaps not as rapid as in S. cerevisiae or Sz. pombe. The identification of the retrotransposons of C. neoformans should assist in the molecular characterization of this important pathogen, and also further our understanding of the role played by retroelements in genome evolution.

Amino Acid Sequence↗

Identification of a testis-specific gene (C15orf2) in the Prader-Willi syndrome region on chromosome 15.

Prader-Willi syndrome (PWS) results from the loss of paternal contributions for a 2-Mb imprinted region on the proximal long arm of human chromosome 15. Hitherto, five paternally active genes have been identified in this region (ZNF127, NDN, MAGEL2, SNURF-SNRPN, and IPW). Here we report the identification of a novel gene in the PWS critical region, which has been designated "chromosome 15 open reading frame 2" (C15orf2). C15orf2 is an intronless gene located between MAGEL2 and SNURF-SNRPN. It is associated with a CpG island, which is methylated in all tissues tested except for germ cells. C15orf2 is transcribed as a 7.5-kb mRNA and contains an open reading frame encoding a predicted 1156-amino-acid protein of unknown function. Transcription of C15orf2 occurs exclusively in the testis, and in adult testis samples, we observed biallelic expression. By zoo-blot analysis, we found related sequences in DNA from other primates, but not in nonprimate DNA. We conclude that C15orf2 may play a role in primate spermatogenesis.

3' Untranslated Regions↗

PIGY, a new plant envelope-class LTR retrotransposon.

Plant LTR retrotransposons of the envelope class define a new branch in the Metaviridae family. They differ from other LTR retrotransposons mainly by the presence of an additional ORF downstream of the gag-pol region which has been hypothesized to be equivalent to the envelope gene of retroviruses. Here we present a newly identified element from pea (Pisum sativum), named PIGY, that has all the features characteristic of this group of LTR retrotransposons. In addition to the potential coding sequence downstream of the gag-pol region, PIGY has a primer binding site complementary to tRNA(asp) and a polypurine tract with a TGGGG motif and is of large size (13,645 bp). The relationship between PIGY and other retrotransposons of the env-class was confirmed by a phylogenetic analysis of their reverse transcriptase domains. One distinctive feature of PIGY is that its env-like region is actually composed of two similar ORFs, each of which encodes a protein with similarity to the Athila envelope-like protein. PIGY is present in the pea genome in 1-5x10(3) copies and is transcriptionally active, suggesting that some of these elements may still be capable of active transposition. Another new env-class retrotransposon similar to PIGY was also identified among genomic sequences of Medicago truncatula.

Amino Acid Sequence↗

Retrotransposon populations of Vicia species with varying genome size.

The (non-LTR) LINE and Ty3-gypsy-type LTR retrotransposon populations of three Vicia species that differ in genome size (Vicia faba, Vicia melanops and Vicia sativa) have been characterised. In each species the LINE retrotransposons comprise a complex, very heterogeneous set of sequences, while the Ty3-gypsy elements are much more homogeneous. Copy numbers of all three retrotransposon groups (Ty1-copia, Ty3-gypsy and LINE) in these species have been estimated by random genomic sequencing and Southern hybridisation analysis. The Ty3-gypsy elements are extremely numerous in all species, accounting for 18-35% of their genomes. The Ty1-copia group elements are somewhat less abundant and LINE elements are present in still lower amounts. Collectively, 20-45% of the genomes of these three Vicia species are comprised of retrotransposons. These data show that the three retrotransposon groups have proliferated to different extents in members of the Vicia genus and high proliferation has been associated with homogenisation of the retrotransposon population.

Blotting, Southern↗

Endogenous retrovirus HERV-I LTR family in primates: sequences, phylogeny, and evolution.

A human endogenous retrovirus (HERV-I; RTVL-I) has been located within the first intron of a haptoglobin-related gene. Two members of the HERV-I family were identified in proximal Yq11.2 and caused AZFa microdeletions as a result of intra-chromosomal recombination events in azoospermic patients. Using PCR25 and the sequencing approach with the genomic DNAs of primates, hominoids, Old and New World monkeys, and prosimians, the HERV-I LTR elements were identified and analysed. The LTR elements were detected only in the hominoids and the Old World monkeys, indicating that the HERV-I LTR elements were inserted into the primate genome after the split of the New World monkeys in the Oligocene era, about 33 million years ago. Nineteen members of the HERV-I LTR elements from the hominoids and the Old World monkeys showed multiple insertions or deletions. They showed a 78.6-97.4% sequence similarity to that of Hu-15 (accession no. AF290422; HERV-I LTR on human Yq11.2). The evolutionary relationships within the HERV-I LTR family among hominoids and Old World monkeys showed a random cluster, indicating that HERV-I LTR elements have evolved independently in primate evolution.

Animals↗

Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5A(m).

Sequencing of a contiguous 215-kb interval of Triticum monococcum showed the presence of five genes in the same order as in previously sequenced colinear barley and rice BACs. Gene 2 was in the same orientation in wheat and rice but inverted in barley. Gene density in this region was 1 gene per 43 kb and the ratio of physical to genetic distance was estimated to be 2,700 kb cM(-1). Twenty more-or-less intact retrotransposons were found in the intergenic regions, covering at least 70% of the sequenced region. The insertion times of 11 retrotransposons were less than 5 million years ago and were consistent with their nested structure. Five new families of retro-elements and the first full-length elements for two additional retrotransposon families were discovered in this region. Significantly higher values of GC content were observed for Triticeae BACs compared with rice BACs. Relative enrichment or depletion of certain dinucleotides was observed in the comparison of introns, exons and retrotransposons. A higher proportion of transitions in CG and CNG sites that are targets for cytosine methylation was observed in retrotransposons (76%) than in introns (37%). These results showed that the wheat genome is a complex mixture of different sequence elements, but with general patterns of content and interspersion that are similar to those seen in maize and barley.

Chromosome Mapping↗

M-MuLV-induced leukemogenesis: integration and structure of recombinant proviruses in tumors.

M-MuLV-specific DNA probes were used to establish the state of integration and amplification of recombinant proviral sequences in Moloney virus-induced tumors of Balb/Mo, Balb/c and 129 mice. The somatically acquired viral sequences contain both authentic M-MuLV genomes and recombinants of M-MuLV with endogenous viral sequences. All reintegrated genomes carry long terminal repeat (LTR) sequences at both termini of their genome. In the preleukemic stage a large population of cells exhibiting a random distribution of reintegrated M-MuLV genomes are seen, but during outgrowth of the tumor, selection of cells occurs leaving one or a few clonal descendants in the outgrown tumor. In this latter stage recombinant genomes can be detected. Although these recombinants constitute a heterogeneous group of proviruses, characteristic molecular markers are conserved among many individual proviral recombinants, lending credence to the notion that a certain recombinant structure is a prerequisite for the onset of neoplasia. The structure of these recombinants shows close structural similarities to the previously described mink cell focus-inducing (MCF)-type viruses.

Animals↗

Characterization of heteroclite subgenomic RNAs associated with PRRSV infection.

In this study, porcine reproductive and respiratory syndrome virus (PRRSV) heteroclite (uncommon forms) RNAs were characterized. Nucleotide sequencing of 11 additional defective RNA species verified that heteroclites are formed between the 5' and 3' termini of PRRSV at short stretches of identity, with variability seen between the junction sites utilized. Northern blot and RT-PCR analyses indicated that heteroclite RNA species were likely to be packaged into purified virions. To study whether heteroclite RNAs and viral genomic RNAs could be packaged into the same virions, PRRSV strain VR-2332 was purified by sucrose density gradient centrifugation. RT-PCR amplification of the viral RNAs isolated from three distinct gradient bands, using genomic- and heteroclite-specific primer pairs, demonstrated that heteroclite RNAs could not be readily dissociated from genomic RNA. Partial segregation of full-length and larger heteroclite genomes to the upper two gradient bands was seen, but smaller species could be found in all three fractions. These results strongly suggest that heteroclite RNAs retain the PRRSV RNA packaging signal. In vitro transcription and translation of one heteroclite cDNA clone verified that the RNA could express a predicted 32.6 kDa protein, indicating that these RNA species have the potential to produce abnormal proteins in infected cells.

Amino Acid Sequence↗

A rare event of insertion polymorphism of a HERV-K LTR in the human genome.

Human endogenous retroviruses (HERVs), which constitute a significant part of the human genome, might have a serious impact on primate evolution. Over a hundred insertions of HERV-K(HML-2) family members distinguish the human genome from other primate genomes. However, only three cases of insertion polymorphisms have been reported so far, all for endogenous HERV-K proviruses. This suggests that some retroviral integrations occurred rather recently in human genome evolution. In this report, we describe a very rare case of true insertion polymorphism of a solitary HERV-K LTR in the human genome. Distribution of the LTR-containing allele was tested in 5 Africans and 83 individuals from three Russian populations. The allele frequency appeared to be relatively high in populations of both European and Asian origin. The detected polymorphic LTR could be a useful molecular genetic marker of the corresponding genomic region.

Africa↗

Characterization of EIAV LTR variability and compartmentalization in various reservoir tissues of long-term inapparent carrier ponies.

Dynamic genomic variation resulting in changes in envelope antigenicity has been established as a fundamental mechanism of persistence by equine infectious anemia virus (EIAV), as observed with other lentiviruses, including HIV-1. In addition to the reported changes in envelope sequences, however, certain studies indicate the viral LTR as a second variable EIAV gene, with the enhancer region being designated as hypervariable. These observations have lead to the suggestion that LTR variation may alter viral replication properties to optimize to the microenvironment of particular tissue reservoirs. To test this hypothesis directly, we examined the population of LTR quasispecies contained in various tissues of two inapparent carrier ponies experimentally infected with a reference EIAV biological clone for 18 months. The results of these studies demonstrated that the EIAV LTR is in fact highly conserved with respect to the infecting LTR species after 1.5 years of persistent infection and regardless of the tissue reservoir. Thus, these comprehensive analyses demonstrate for the first time that the EIAV LTR is highly conserved during long-term persistent infection and that the observed variations in viral LTR are associated more with in vitro adaptation to replication in cultured cells rather than in vivo replication in natural target cells.

Animals↗

Origin of a substantial fraction of human regulatory sequences from transposable elements.

Transposable elements (TEs) are abundant in mammalian genomes and have potentially contributed to their hosts' evolution by providing novel regulatory or coding sequences. We surveyed different classes of regulatory region in the human genome to assess systematically the potential contribution of TEs to gene regulation. Almost 25% of the analyzed promoter regions contain TE-derived sequences, including many experimentally characterized cis-regulatory elements. Scaffold/matrix attachment regions (S/MARs) and locus control regions (LCRs) that are involved in the simultaneous regulation of multiple genes also contain numerous TE-derived sequences. Thus, TEs have probably contributed substantially to the evolution of both gene-specific and global patterns of human gene regulation.

5' Untranslated Regions↗

Optimisation of interdelta analysis for Saccharomyces cerevisiae strain characterisation.

A new primer pair (delta12-delta21) for polymerase chain reaction-based yeast typing was designed using the yeast genome sequence. The specificity of this primer pair was checked by the comparison of the electrophoresis pattern with a virtual profile calculated from Blast data. The analysis of 53 commercial and laboratory Saccharomyces cerevisiae yeast strains showed a clear improvement of interdelta analysis using the newly designed primers.

Base Sequence↗

Sequence and genetic analyses of the 3' terminus and integration sites of the RIII/Sa mouse mammary tumor (MMTV) exogenous provirus.

The RIII/Sa mouse mammary tumor virus (MMTV) is one of several exogenous MMTV viruses transmitted to suckling mice through the milk. We report herein the nucleotide sequence of the exogenous RIII/Sa provirus from the central Eco RI site through to the end of the U5 region encoded by the 3' LTR. We also provide a detailed sequence analysis often different 3' terminal exogenous MMTV proviral integration sites within mammary tumor DNA obtained by the technique of genome walking. Using a combination of Southern blotting with 3' end probes and PCR utilizing a unique RIII/Sa specific 3' primer, we confirm that the RIII/Sa provirus integrates multiple times in mouse mammary tumors but that little or no integration occurs in various normal tissues. Southern blotting analyses with 3' end probes also indicate that RIII/Sa mice contain two additional endogenous MMTV loci, mtv-6 and mtv- 17, not previously reported. The combined genetic analyses reported herein distinguish between exogenous proviral integrants and endogenous germline MMTV.

Animals↗