Expression pattern analysis of transcribed HERV sequences is complicated by ex vivorecombination

Flockerzi, Aline; Maydt, Jochen; Frank, Oliver; Ruggieri, Alessia; Maldener, Esther; Seifarth, Wolfgang; Medstrand, Patrik; Lengauer, Thomas; Meyerhans, Andreas; Leib-Mösch, Christine; Meese, Eckart; Mayer, Jens

doi:10.1186/1742-4690-4-39

Cited by 19 publications

(35 citation statements)

References 35 publications

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“…Analysis of HK2 env sequences found in the supernatants of the NCCIT cell line, but not other cell lines, revealed evidence of virus diversity and recombination, suggesting that the HK2 genome replicated through reverse transcription (unpublished data). It is possible that ex vivo RT-PCR recombination artificially created these recombinant HK2 env sequences detected in our study (68). However, the detection of recombinant env sequences (45% of the sequences) only in the supernatants of NCCIT cells, but not other cell lines, argues that these recombinant env sequences arose by HK2 replication through reverse transcription in the NCCIT cells and not artifactually.…”

Section: Resultsmentioning

confidence: 70%

Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K–Related Sequences

Contreras-Galindo

Kaplan

Dube

et al. 2015

J Virol

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Human endogenous retroviruses (HERV) make up 8% of the human genome. While the youngest of these retroviruses, HERV-K(HML-2), termed HK2, is able to code for all viral proteins and produce virus-like particles, it is not known if these virus particles package and transmit HK2-related sequences. Here, we analyzed the capacity of HK2 for packaging and transmitting HK2 sequences. We created an HK2 probe, termed Bogota, which can be packaged into HK2 viruses, and transfected it into cells that make HK2 particles. Supernatants of the transfected cells, which contained HK2 viral particles, then were added to target cells, and the transmissibility of the HK2 Bogota reporter was tracked by G418 resistance. Our studies revealed that contemporary HK2 virions produced by some teratocarcinoma and breast cancer cell lines, as well as by peripheral blood lymphocytes from lymphoma patients, can package HK2 Bogota probes, and these viruses transmitted these probes to other cells. After transmission, HK2 Bogota transcripts undergo reverse transcription, a step impaired by antiretroviral agents or by introduction of mutations into the probe sequences required for reverse transcription. HK2 viruses were more efficiently transmitted in the presence of HK2 Rec or HIV-1 Tat and Vif. Transmitted Bogota probes formed episomes but did not integrate into the cellular genome. Resistance to integration might explain the relatively low number of HK2 insertions that were acquired during the last 25 million years of evolution. Whether transient transmission of modern HK2 sequences, which encode two putative oncoproteins, can lead to disease remains to be studied. IMPORTANCERetroviruses invaded the genome of human ancestors over the course of millions of years, yet these viruses generally have been inactivated during evolution, with only remnants of these infectious sequences remaining in the human genome. One of these viruses, termed HK2, still is capable of producing virus particles, although these particles have been regarded as being noninfectious. Using a genetic probe derived from HK2, we have discovered that HK2 viruses produced in modern humans can package HK2 sequences and transmit them to various other cells. Furthermore, the genetic sequences packaged in HK2 undergo reverse transcription. The transmitted probe circularized in the cell and failed to integrate into the cellular genome. These findings suggest that modern HK2 viruses can package viral RNA and transmit it to other cells. Contrary to previous views, we provide evidence of an extracellular viral phase of modern HK2 viruses. We have no evidence of sustained, spreading infection.A ctively replicating retroviruses infected the germ line multiple times over the millions of years of human evolution. These sequences were transmitted vertically in a Mendelian fashion to the next generation; therefore, they became a stable part of the inherited genetic material. Relics of these retroviral infections presently make up approximately 8% of the modern human genome. These retro...

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Section: Resultsmentioning

confidence: 70%

Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K–Related Sequences

Contreras-Galindo

Kaplan

Dube

et al. 2015

J Virol

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“…In total, ϳ92% of all generated se-quences could be unambiguously mapped to a specific HERV-W locus (Table 2; see Table S1 in the supplemental material). We interpret the remaining 8% of unassigned sequences as reads with unrecognized sequencing artifacts or potential recombinants of transcripts from different HERV-W loci generated during RT-PCR (20,44).…”

Section: Resultsmentioning

confidence: 99%

“…We chose a direct approach in those studies by generating cDNA sequences from RNA transcripts from HERV loci and reassigning those cDNA sequences to specific HERV loci. Such a strategy not only identifies HERV loci actually transcribed, but also generates data on relative transcription levels of HERV loci (35,44,50). Using this strategy, we recently also investigated the transcription of HERV-W in PBMC and identified a total of seven loci as being transcribed.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Human Endogenous Retrovirus Group HERV-W Locus Transcription in Multiple Sclerosis Brain Lesions by High-Throughput Amplicon Sequencing

Schmitt

Richter

Backes

et al. 2013

J Virol

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“…The sequence assignment strategy and the Locus-Assigner software were previously discussed in more detail (19). cDNA sequences with more than 17 mismatches to the bestmatching reference proviral sequence were excluded from further analysis because they very likely represent recombined cDNAs from different proviral transcripts that arose ex vivo during cDNA generation (18).…”

Section: Methodsmentioning

confidence: 99%

Human Endogenous Retrovirus Family HERV-K(HML-2) RNA Transcripts Are Selectively Packaged into Retroviral Particles Produced by the Human Germ Cell Tumor Line Tera-1 and Originate Mainly from a Provirus on Chromosome 22q11.21

Ruprecht

Ferreira

Flockerzi

et al. 2008

J Virol

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The human germ cell tumor line Tera-1 produces retroviral particles which are encoded by the human endogenous retrovirus family HERV-K(HML-2). We show here, by quantitative reverse transcriptase PCR, that HML-2 gag and env RNA transcripts are selectively packaged into Tera-1 retroviral particles, whereas RNAs from cellular housekeeping genes and from other HERV families (HERV-H and HERV-W) are nonselectively copackaged. Assignment of cloned HML-2 gag and env cDNAs from Tera-1 retroviral particles to individual HML-2 loci in the human genome demonstrated that HML-2 RNA transcripts packaged into Tera-1 retroviral particles originate almost exclusively from an HML-2 provirus on chromosome 22q11.21. Based on relative cloning frequencies, this provirus was the most active among a total of eight transcribed HML-2 loci identified in Tera-1 cells. These data suggest that at least one HML-2 element, that is, the HML-2 provirus on 22q11.21, has retained the capacity for packaging RNA into HML-2-encoded retroviral particles. Given its elevated transcriptional activity and the presence of a full-length Gag open reading frame, the 22q11.21 HML-2 provirus may also significantly contribute to Gag protein and thus particle production in Tera-1 cells. Our findings provide important clues to the generation and biological properties of HML-2-encoded particles. In addition, copackaging of non-HML-2 HERV transcripts in HML-2-encoded particles should inform the debate about endogenous retroviral particles putatively encoded by non-HML-2 HERV families that have previously been described for other human diseases, such as multiple sclerosis.

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Expression pattern analysis of transcribed HERV sequences is complicated by ex vivorecombination

Cited by 19 publications

References 35 publications

Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K–Related Sequences

Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K–Related Sequences

Comprehensive Analysis of Human Endogenous Retrovirus Group HERV-W Locus Transcription in Multiple Sclerosis Brain Lesions by High-Throughput Amplicon Sequencing

Human Endogenous Retrovirus Family HERV-K(HML-2) RNA Transcripts Are Selectively Packaged into Retroviral Particles Produced by the Human Germ Cell Tumor Line Tera-1 and Originate Mainly from a Provirus on Chromosome 22q11.21

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