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Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination.

Flockerzi A, Maydt J, Frank O, Ruggieri A, Maldener E, Seifarth W, Medstrand P, Lengauer T, Meyerhans A, Leib-Mösch C, Meese E, Mayer J - Retrovirology (2007)

Bottom Line: A number of loci of the HERV-K(HML-2) family are evolutionarily much younger.Isolating such a variant from human individuals would be a significant finding for human biology.Further complicated by an unknown amount of allelic sequence variation in HERV-K(HML-2) proviruses, newly identified HERV-K(HML-2) variants should be interpreted very cautiously.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Genetics, Medical Faculty, University of Saarland, Homburg, Germany. aline.flockerzi@uniklinik-saarland.de

ABSTRACT

Background: The human genome comprises numerous human endogenous retroviruses (HERVs) that formed millions of years ago in ancestral species. A number of loci of the HERV-K(HML-2) family are evolutionarily much younger. A recent study suggested an infectious HERV-K(HML-2) variant in humans and other primates. Isolating such a variant from human individuals would be a significant finding for human biology.

Results: When investigating expression patterns of specific HML-2 proviruses we encountered HERV-K(HML-2) cDNA sequences without proviral homologues in the human genome, named HERV-KX, that could very well support recently suggested infectious HML-2 variants. However, detailed sequence analysis, using the software RECCO, suggested that HERV-KX sequences were produced by recombination, possibly arising ex vivo, between transcripts from different HML-2 proviral loci.

Conclusion: As RT-PCR probably will be instrumental for isolating an infectious HERV-K(HML-2) variant, generation of "new" HERV-K(HML-2) sequences by ex vivo recombination seems inevitable. Further complicated by an unknown amount of allelic sequence variation in HERV-K(HML-2) proviruses, newly identified HERV-K(HML-2) variants should be interpreted very cautiously.

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RECCO-based explanation of HERV-KX sequences as recombination products. Based on RECCO analysis, HERV-KX sequences can be explained as recombination products between transcripts from different HML-2 proviral loci. Three examples of HERV-KX sequences were multiply aligned with HML-2 proviral sequences, the transcripts of which served as template for recombination events. HERV-KX sequence "93" was generated by one recombination event involving two loci. HERV-KX sequence "B270" was generated by two recombination events involving three loci. HERV-KX sequence "94" was generated by two recombination events involving two different proviral templates. Probable recombination regions are indicated by medium grey background. Light and dark grey background indicates proviral templates. Localization of the RT-PCR amplicon and the 96 bp sequence (see text) within the HML-2 gag gene/provirus is depicted above the sequence comparisons.
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Figure 2: RECCO-based explanation of HERV-KX sequences as recombination products. Based on RECCO analysis, HERV-KX sequences can be explained as recombination products between transcripts from different HML-2 proviral loci. Three examples of HERV-KX sequences were multiply aligned with HML-2 proviral sequences, the transcripts of which served as template for recombination events. HERV-KX sequence "93" was generated by one recombination event involving two loci. HERV-KX sequence "B270" was generated by two recombination events involving three loci. HERV-KX sequence "94" was generated by two recombination events involving two different proviral templates. Probable recombination regions are indicated by medium grey background. Light and dark grey background indicates proviral templates. Localization of the RT-PCR amplicon and the 96 bp sequence (see text) within the HML-2 gag gene/provirus is depicted above the sequence comparisons.

Mentions: Using RECCO, we analysed HERV-KX sequences in comparison to respective HML-2 proviral sequences in the human genome. All HERV-KX sequences were predicted by RECCO to consist of two to three different HML-2 proviral sequences, thus having undergone one or two, respectively, recombination events. For two sequences, alternative predictions, further reducing the number of nucleotide differences, involved four different proviruses, thus involving three recombination events (Table 2). Recombinations within three exemplary cDNA sequences can be portrayed as follows. HERV-KX sequence "B270", displaying 39 nt differences to its best match, was predicted to be comprised of sequences from a provirus on chromosome 7 and two different proviruses on chromosome 3. Recombinations were predicted to have occured between nt 267 and 273 and between nt 583 to 712 of the cDNA, resulting in an explanation with zero nt differences. HERV-KX sequence "94", displaying 26 nt differences to its best matching provirus on human chromosome 11, was predicted to be comprised of sequences from HML-2 proviruses on chromosomes 7 and 11. Recombination events were predicted to have occured between nt 415 and 422, and between nt 583 and 651, resulting in an explanation with zero nt differences. Finally, HERV-KX sequence "93", displaying 13 nt differences to its best match, was predicted to be comprised of proviruses on human chromosome 7 and 21, with a recombination between nt 583–610, and resulting in an explanation with 1 nt difference remaining (Figures 2 and 3). For all HERV- KX sequences, on average 35 (SD 15.5) nt differences could be reduced to 2.6 (SD 3.4) nt differences when considering RECCO predictions for recombinations. Those numbers are in ranges typically observed in our analysis for best matches of assignable sequences, where, on average, 4.5 (SD 3.7) nt differences remained between cDNA and best match. Of further note, because we defined HERV-KX sequences as displaying 18 or more nt differences to the best match, it is possible that there are further recombined cDNAs with corresponding signals among the sequences with <18 nt differences.


Expression pattern analysis of transcribed HERV sequences is complicated by ex vivo recombination.

Flockerzi A, Maydt J, Frank O, Ruggieri A, Maldener E, Seifarth W, Medstrand P, Lengauer T, Meyerhans A, Leib-Mösch C, Meese E, Mayer J - Retrovirology (2007)

RECCO-based explanation of HERV-KX sequences as recombination products. Based on RECCO analysis, HERV-KX sequences can be explained as recombination products between transcripts from different HML-2 proviral loci. Three examples of HERV-KX sequences were multiply aligned with HML-2 proviral sequences, the transcripts of which served as template for recombination events. HERV-KX sequence "93" was generated by one recombination event involving two loci. HERV-KX sequence "B270" was generated by two recombination events involving three loci. HERV-KX sequence "94" was generated by two recombination events involving two different proviral templates. Probable recombination regions are indicated by medium grey background. Light and dark grey background indicates proviral templates. Localization of the RT-PCR amplicon and the 96 bp sequence (see text) within the HML-2 gag gene/provirus is depicted above the sequence comparisons.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC1904241&req=5

Figure 2: RECCO-based explanation of HERV-KX sequences as recombination products. Based on RECCO analysis, HERV-KX sequences can be explained as recombination products between transcripts from different HML-2 proviral loci. Three examples of HERV-KX sequences were multiply aligned with HML-2 proviral sequences, the transcripts of which served as template for recombination events. HERV-KX sequence "93" was generated by one recombination event involving two loci. HERV-KX sequence "B270" was generated by two recombination events involving three loci. HERV-KX sequence "94" was generated by two recombination events involving two different proviral templates. Probable recombination regions are indicated by medium grey background. Light and dark grey background indicates proviral templates. Localization of the RT-PCR amplicon and the 96 bp sequence (see text) within the HML-2 gag gene/provirus is depicted above the sequence comparisons.
Mentions: Using RECCO, we analysed HERV-KX sequences in comparison to respective HML-2 proviral sequences in the human genome. All HERV-KX sequences were predicted by RECCO to consist of two to three different HML-2 proviral sequences, thus having undergone one or two, respectively, recombination events. For two sequences, alternative predictions, further reducing the number of nucleotide differences, involved four different proviruses, thus involving three recombination events (Table 2). Recombinations within three exemplary cDNA sequences can be portrayed as follows. HERV-KX sequence "B270", displaying 39 nt differences to its best match, was predicted to be comprised of sequences from a provirus on chromosome 7 and two different proviruses on chromosome 3. Recombinations were predicted to have occured between nt 267 and 273 and between nt 583 to 712 of the cDNA, resulting in an explanation with zero nt differences. HERV-KX sequence "94", displaying 26 nt differences to its best matching provirus on human chromosome 11, was predicted to be comprised of sequences from HML-2 proviruses on chromosomes 7 and 11. Recombination events were predicted to have occured between nt 415 and 422, and between nt 583 and 651, resulting in an explanation with zero nt differences. Finally, HERV-KX sequence "93", displaying 13 nt differences to its best match, was predicted to be comprised of proviruses on human chromosome 7 and 21, with a recombination between nt 583–610, and resulting in an explanation with 1 nt difference remaining (Figures 2 and 3). For all HERV- KX sequences, on average 35 (SD 15.5) nt differences could be reduced to 2.6 (SD 3.4) nt differences when considering RECCO predictions for recombinations. Those numbers are in ranges typically observed in our analysis for best matches of assignable sequences, where, on average, 4.5 (SD 3.7) nt differences remained between cDNA and best match. Of further note, because we defined HERV-KX sequences as displaying 18 or more nt differences to the best match, it is possible that there are further recombined cDNAs with corresponding signals among the sequences with <18 nt differences.

Bottom Line: A number of loci of the HERV-K(HML-2) family are evolutionarily much younger.Isolating such a variant from human individuals would be a significant finding for human biology.Further complicated by an unknown amount of allelic sequence variation in HERV-K(HML-2) proviruses, newly identified HERV-K(HML-2) variants should be interpreted very cautiously.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Human Genetics, Medical Faculty, University of Saarland, Homburg, Germany. aline.flockerzi@uniklinik-saarland.de

ABSTRACT

Background: The human genome comprises numerous human endogenous retroviruses (HERVs) that formed millions of years ago in ancestral species. A number of loci of the HERV-K(HML-2) family are evolutionarily much younger. A recent study suggested an infectious HERV-K(HML-2) variant in humans and other primates. Isolating such a variant from human individuals would be a significant finding for human biology.

Results: When investigating expression patterns of specific HML-2 proviruses we encountered HERV-K(HML-2) cDNA sequences without proviral homologues in the human genome, named HERV-KX, that could very well support recently suggested infectious HML-2 variants. However, detailed sequence analysis, using the software RECCO, suggested that HERV-KX sequences were produced by recombination, possibly arising ex vivo, between transcripts from different HML-2 proviral loci.

Conclusion: As RT-PCR probably will be instrumental for isolating an infectious HERV-K(HML-2) variant, generation of "new" HERV-K(HML-2) sequences by ex vivo recombination seems inevitable. Further complicated by an unknown amount of allelic sequence variation in HERV-K(HML-2) proviruses, newly identified HERV-K(HML-2) variants should be interpreted very cautiously.

Show MeSH
Related in: MedlinePlus