Analysis of retrotransposon families in genomic DNA by two-dimensional restriction mapping: detection of VL30 insertions in mouse thymic lymphoma

Genomic analysis of mouse VL30 retrotransposons

BACKGROUND

Retrotransposons are mobile elements that have a high impact on shaping the mammalian genomes. Since the availability of whole genomes, genomic analyses have provided novel insights into retrotransposon biology. However, many retrotransposon families and their possible genomic impact have not yet been analysed.

RESULTS

Here, we analysed the structural features, the genomic distribution and the evolutionary history of mouse VL30 LTR-retrotransposons. In total, we identified 372 VL30 sequences categorized as 86 full-length and 49 truncated copies as well as 237 solo LTRs, with non-random chromosomal distribution. Full-length VL30s were highly conserved elements with intact retroviral replication signals, but with no protein-coding capacity. Analysis of LTRs revealed a high number of common transcription factor binding sites, possibly explaining the known inducible and tissue-specific expression of individual elements. The overwhelming majority of full-length and truncated elements (82/86 and 40/49, respectively) contained one or two specific motifs required for binding of the VL30 RNA to the poly-pyrimidine tract-binding protein-associated splicing factor (PSF). Phylogenetic analysis revealed three VL30 groups with the oldest emerging ~17.5 Myrs ago, while the other two were characterized mostly by new genomic integrations. Most VL30 sequences were found integrated either near, adjacent or inside transcription start sites, or into introns or at the 3' end of genes. In addition, a significant number of VL30s were found near Krueppel-associated box (KRAB) genes functioning as potent transcriptional repressors.

CONCLUSION

Collectively, our study provides data on VL30s related to their: (a) number and structural features involved in their transcription that play a role in steroidogenesis and oncogenesis; (b) evolutionary history and potential for retrotransposition; and (c) unique genomic distribution and impact on gene expression.

SV40 large T antigen up-regulates the retrotransposition frequency of viral-like 30 elements

The regulation of non-autonomous retrotransposition is not known. A recombinant bearing a hygromycin gene and a viral-like 30 (VL30) retrotransposon tagged with an enhanced green fluorescent protein (EGFP) gene-based retrotransposition cassette was constructed and used for detection of retrotransposition events. Transfection of this recombinant produced retrotransposition events, detected both by EGFP fluorescence and PCR analysis, in hygromycin-selected clones of two established simian virus 40 (SV40)-transformed mouse NIH3T3 cell lines but not in normal NIH3T3 cells. The retrotransposition potential of this recombinant, as a provirus, was studied in stably transfected NIH3T3 clones. Transfection of these clones with either a wild-type or a mutant LE1135T SV40 large T antigen gene, not expressing small t protein, induced retrotransposition events at high frequencies as measured by fluorescence-activated cell scanning (FACS). In addition, measuring retrotransposition frequencies over a period of nine days following infection with isolated SV40 particles, revealed that the frequency of retrotransposition was time-dependent and induced as early as 24 h, increasing exponentially to high levels (>10(-2) events per cell per generation) up to nine days post-infection. Furthermore, ectopic expression of a cloned MoMLV-reverse transcriptase gene also produced retrotransposition events and suggested that the large T antigen most likely acted through induction of expression of endogenous reverse transcriptase genes. Our results show a direct correlation between SV40-cell transformation and VL30 retrotransposition and provide for the first time strong evidence that SV40 large T antigen up-regulates the retrotransposition of VL30 elements.

Clone-specific high-frequency retrotransposition of a recombinant virus containing a VL30 promoter in SV40-transformed NIH3T3 cells

A recombinant virus, containing the promoter of a VL30 LTR and tagged with the neomycin gene as a selection and indicator marker, was constructed to investigate transposition events in NIH3T3 cells after SV40 transformation. This retroviral construct was transfected into psi/CRE packaging cells, and pseudovirions were used to infect NIH3T3 cells. Clones resistant to G418 bearing single-copy integrations of the recombinant virus were isolated and transformed by SV40 virus. Transpositions were detected through RFLPs with a neomycin probe and 'retrotransposition' was further confirmed by inverse PCR and DNA sequencing of transposed and parental copies. We found that: (1) retrotransposition of this recombinant virus occurred with a high frequency in a parental clone transformed with SV40 virus suggesting that the frequency of retrotransposition depended on the initial site of provirus integration; (2) the transposition frequency was independent of the transcription level of the recombinant construct; and (3) analysis of transposition-positive transformants showed that the high transposition frequency appeared to be associated with the induction of endogenous reverse transcriptases.