Characterization of unintegrated retroviral DNA with long terminal repeat-associated cell-derived inserts

Extending gene ontology in the context of extracellular RNA and vesicle communication

Background

To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research.

Methods

By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO. In addition, we have initiated an ongoing process of extractions of gene product annotations associated with these terms from Vesiclepedia and ExoCarta, conversion of the extracted annotations to Gene Association File (GAF) format for batch submission to GO, and curation of the submitted annotations by the GO Consortium. As a use case, we have incorporated some of the GO terms into annotations of samples from the exRNA Atlas and implemented a faceted search interface based on such annotations.

Results

We have added 7 new terms and modified 9 existing terms (along with their synonyms and relationships) to GO. Additionally, 18,695 unique coding gene products (mRNAs and proteins) and 963 unique non-coding gene products (ncRNAs) which are associated with the terms: “extracellular vesicle”, “extracellular exosome”, “apoptotic body”, and “microvesicle” were extracted from ExoCarta and Vesiclepedia. These annotations are currently being processed for submission to GO.

Conclusions

As an inter-community effort, we have made a substantial update to GO in the exRNA context. We have also demonstrated the utility of some of the new GO terms for sample annotation and metadata search.

Virion packaging determinants and reverse transcription of SRP RNA in HIV-1 particles

Diverse retroviruses have been shown to package host SRP (7SL) RNA. However, little is known about the viral determinants of 7SL RNA packaging. Here we demonstrate that 7SL RNA is more selectively packaged into HIV-1 virions than are other abundant Pol-III-transcribed RNAs, including Y RNAs, 7SK RNA, U6 snRNA and cellular mRNAs. The majority of the virion-packaged 7SL RNAs were associated with the viral core structures and could be reverse-transcribed in HIV-1 virions and in virus-infected cells. Viral Pol proteins influenced tRNAlys,3 packaging but had little influence on virion packaging of 7SL RNA. The N-terminal basic region and the basic linker region of HIV-1 NCp7 were found to be important for efficient 7SL RNA packaging. Although Alu RNAs are derived from 7SL RNA and share the Alu RNA domain with 7SL RNA, the packaging of Alu RNAs was at least 50-fold less efficient than that of 7SL RNA. Thus, 7SL RNAs are selectively packaged into HIV-1 virions through mechanisms distinct from those for viral genomic RNA or primer tRNAlys,3. Virion packaging of both human cytidine deaminase APOBEC3G and cellular 7SL RNA are mapped to the same regions in HIV-1 NC domain.

Effects of identity minimization on Moloney murine leukemia virus template recognition and frequent tertiary template-directed insertions during nonhomologous recombination

Homology requirements for Moloney murine leukemia virus recombination were addressed in this study by monitoring titer defects observed when acceptor/donor template identity lengths were systematically reduced. Recombination acceptors with at least 16 contiguous bases of donor template identity were recognized as efficiently as longer acceptors. In contrast, a sharp 1-log titer drop was observed for an acceptor of only 15 bases long, with an additional 1-log titer decline for an 8-base acceptor and further decreases for shorter acceptors. Eighty-three independent nonhomologous recombination products were sequenced to examine recombination template selection in the absence of significant sequence identity. These replication products contained a total of 152 nonhomologous crossover junctions. Forced copy choice models predict that forced nonhomologous recombination should result in DNA synthesis to the donor template's 5' end, followed by microidentity-guided acceptor template selection. However, only a single product displayed this structure. The majority of examined nonhomologous recombination products contained junction-associated sequence insertions. Most insertions resulted from the use of one or more tertiary templates, recognizable as discontiguous portions of viral or host RNA or minus-strand DNA. The donor/acceptor template microidentity evident at most crossovers reconfirmed the remarkable capability of the reverse transcription machinery to recognize short regions of sequence identity. These results demonstrate that recruitment of discontiguous host or viral sequences is a common way for retroviruses to resolve nonhomologous recombination junctions and provide experimental support for the role of splinting templates in the generation of retroviral insertions.

Evidence for the acquisition of multi-drug resistance in an HIV-1 clinical isolate via human sequence transduction

Insertions in HIV-1 reverse transcriptase's fingers subdomain can enhance chain terminator excision and confer resistance to multiple nucleoside analogs. Inserts that resemble flanking sequences likely arise by local sequence duplication. However, a remarkable variety of non-repeat fingers insertions have been observed. Here, molecular epidemiology, sequence analyses and mechanistic modeling were employed to show that one Japanese isolate's RT fingers insert likely resulted from non-homologous recombination between virus and host sequences and the transductive copying of 37 nucleotides from human chromosome 17. These findings provide evidence that human sequence transduction can, at least rarely, contribute to genetic and phenotypic variation in pandemic HIV.

Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes

Retroviruses specifically package two copies of their RNA genome in each viral particle, along with some small cellular RNAs, including tRNAs and 7S L RNA. We show here that Rous sarcoma virus (RSV) also packages U6 snRNA at approximately one copy per virion. In addition, trace amounts of U1 and U2 snRNAs were detected in purified virus by Northern blotting. U6 snRNA comigrated with the RSV 70S genomic RNA dimer on sucrose gradients. We observed reverse transcription of U6 snRNA in an endogenous reaction in which RSV particles were the source of both reverse transcriptase and RNA substrates. This finding led us to examine mammalian genomic sequences for the presence of snRNA pseudogenes. A survey of the human, mouse, and rat genomes revealed a high number of spliceosomal snRNA pseudogenes. U6 pseudogenes were the most abundant, with approximately 200 copies in each genome. In the human genome, 67% of U6 snRNA pseudogenes, and a significant number of the other snRNA pseudogenes, were associated with LINE, SINE, or retroviral LTR repeat sequences. We propose that the packaging of snRNAs in retroviral particles leads to their reverse transcription in an infected cell and the integration of snRNA/viral recombinants into the host genome.

Nontemplated base addition by HIV-1 RT can induce nonspecific strand transfer in vitro

After minus-strand strong-stop DNA (-sssDNA) synthesis, the RNA template is degraded by the RNase H activity of reverse transcriptase (RT), generating a single-stranded DNA. The genomes of some retroviruses contain sequences that could lead to self-priming of their minus signsssDNA. Self-priming was prevented by annealing a DNA oligonucleotide to the 3' end of model DNAs that corresponded to the 3' ends of the -sssDNAs (-R ssDNA) from human immunodeficiency virus type 1 (HIV-1), type 2 (HIV-2), and human T-cell leukemia virus type 1 (HTLV-1) but nonspecific strand transfer to ssDNA molecules in solution was induced in vitro (Golinelli and Hughes, 2001). This nonspecific strand transfer involved the addition of a nontemplated base to the 3' end of -R ssDNAs that was part of a blunt-ended duplex. In the case of HIV-2 -R ssDNA, A and C were added more efficiently than G and T. Strand transfer to ssDNA in solution occurred only if the nontemplated base could form a basepair with the last base at the 3' end of the ssDNA. If there was a mismatch, strand transfer did not occur. There was no detectable strand transfer to internal sites in the target ssDNA except to the second position from the 3' end of the DNA acceptor when the sequences at the 3' ends of the two DNAs allowed the formation of two basepairs. The nontemplated base addition and the one-basepair strand transfer were both affected by the salt concentration in the reaction, the nature of the reverse transcriptase (HIV-1 versus Moloney murine leukemia virus), and the sequence at the 3' end of -R ssDNA. NC reduced the efficiency of nonspecific strand transfer in vitro, suggesting that NC may have a role in reducing nonspecific strand transfer in vivo.

Characterization of the block in replication of nucleocapsid protein zinc finger mutants from moloney murine leukemia virus

Mutagenesis studies have shown that retroviral nucleocapsid (NC) protein Zn(2+) fingers (-Cys-X(2)-Cys-X(4)-His-X(4)-Cys- [CCHC]) perform multiple functions in the virus life cycle. Moloney murine leukemia virus mutants His 34-->Cys (CCCC) and Cys 39-->His (CCHH) were able to package their genomes normally but were replication defective. Thermal dissociation experiments showed that the CCHH mutant was not defective in genomic RNA dimer structure. Primer tRNA placement on the viral genome and the ability of the tRNA to function in reverse transcription initiation in vitro also appear normal. Some "full-length" DNA copies of the viral genome were synthesized in mutant virus-infected cells. The CCCC and CCHH mutants produced these DNA copies at greatly reduced levels. Circle junction fragments, amplified from two-long-terminal-repeat viral DNA (vDNA) by PCR, were cloned and characterized. Remarkably, it was discovered that vDNA isolated from cells infected with mutant virions had a wide variety of abnormalities at the site at which the two ends of the linear precursor had been ligated to form the circle (i.e., the junction between the 5' end of U3 and the 3' end of U5). In some molecules, bases were missing from regions corresponding to the U3 and U5 linear vDNA termini; in others, the viral sequences extended either beyond the U5 sequences into the primer-binding site and 5' leader or beyond the U3 sequences into the polypurine tract into the env coding region. Still other molecules contained nonviral sequences between the linear vDNA termini. Such defective genomes would certainly be unsuitable substrates for integration. Thus, strict conservation of the CCHC structure in NC is required for infection events prior to and possibly including integration.

Utilization of nonhomologous minus-strand DNA transfer to generate recombinant retroviruses

During reverse transcription, minus-strand DNA transfer connects the sequences located at the two ends of the viral RNA to generate a long terminal repeat. It is thought that the homology in the repeat (R) regions located at the two ends of the viral RNA sequences facilitate minus-strand DNA transfer. In this report, the effects of diminished R-region homology on DNA synthesis and virus titer were examined. A retrovirus vector, PY31, was constructed to contain the 5' and 3' cis-acting elements from Moloney murine sarcoma virus and spleen necrosis virus. These two viruses are genetically distinct, and the two R regions contain little homology. In one round of replication, the PY31 titer was approximately 3,000-fold lower than that of a control vector with highly homologous R regions. The molecular characteristics of the junctions of minus-strand DNA transfer were analyzed in both unintegrated DNA and integrated proviruses. Short stretches of homology were found at the transfer junctions and were likely to be used to facilitate minus-strand DNA transfer. Both minus-strand strong-stop DNA and weak-stop DNA were observed to mediate strand transfer. The ability of PY31 to complete reverse transcription indicates that minus-strand DNA transfer can be used to join sequences from two different viruses to form recombinant viruses. These results suggest the provocative possibility that genetically distinct viruses can interact through this mechanism.

Premature strand transfer by the HIV-1 reverse transcriptase during strong-stop DNA synthesis

Reverse transcription of retroviral genomes starts near the 5' end of the viral RNA by use of an associated tRNA primer. According to the current model of reverse transcription, the initial cDNA product, termed minus-strand strong-stop DNA, 'jumps' to a repeated sequence (R region) at the 3' end of the RNA template. The human retroviruses have relatively long R regions (97-247 nucleotides) when compared to murine and avian viruses (16-68 nucleotides). This suggests that the full complement of the R region is not required for strand transfer and that partial cDNA copies of the 5' R can prematurely jump to the 3' R. To test this hypothesis, we generated mutants of the human immunodeficiency virus with R region changes and analyzed whether 5' or 3' R sequences were inherited by the progeny. We found that in most cases, 5' R-encoded sequences are dominant, which is consistent with the model of reverse transcription. Using a selection protocol, however, we were also able to identify progeny viruses with R sequences derived from the original 3' R element. These results suggest that partial strong stop cDNAs can be transferred with R region homologies much shorter than 97 nucleotides.

A model system for nonhomologous recombination between retroviral and cellular RNA

A current model for the generation of transforming retroviruses proposes that read-through RNAs, containing both viral and cellular sequences, are copackaged with viral genomic RNA. It is, however, possible that a cellular mRNA is occasionally encapsidated into a retroviral particle, even though viral packaging sequences are absent. We have generated recombinant proviruses following copackaging of an avian leukosis viral genomic RNA and a neo-containing RNA completely devoid of retroviral sequences. In these studies, we used the packaging cell line SE21Q1b, which has the unique ability to randomly package cellular mRNA into retroviral particles. We describe 10 recombinants obtained following copackaging of nonhomologous RNAs. Our data show that recombination is not occurring at the DNA level in the parental SE21Q1b cells but is occurring at the RNA level, during reverse transcription. These data further suggest that reverse transcriptase can preferentially jump between templates at short stretches of homology in otherwise unrelated RNAs. We conclude that retroviral sequences are not required for packaged mRNA to be reverse transcribed and to be included in integrated proviruses.

Recent advances in retrovirus vector technology

Retroviral vectors are widely used for the study of retroviral replication and to introduce DNA into somatic cells. An exciting new approach in retroviral vector technology is the use of internal ribosome entry sites from picornaviruses to provide stable expression of multiple genes. In addition, strategies are being developed that target the expression of retroviral vectors to specific cell populations.