title: Genomic analysis of mouse VL30 retrotransposons.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece ; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (IMBB-FORTH), University Campus, Ioannina, 45110 Greece.
authors.forename: Georgios
authors.initials: G
authors.lastname: Markopoulos
authors.affiliation: Laboratory of Molecular Biology and Genetics, Department of Biological Applications and Technology, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Noutsopoulos
authors.affiliation: Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece.
authors.forename: Stefania
authors.initials: S
authors.lastname: Mantziou
authors.affiliation: Department of Computer Science, School of Sciences, University of Ioannina, Ioannina, 45110 Greece.
authors.forename: Demetrios
authors.initials: D
authors.lastname: Gerogiannis
authors.affiliation: Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece.
authors.forename: Soteroula
authors.initials: S
authors.lastname: Thrasyvoulou
authors.affiliation: Hematology Laboratory, Unit of Molecular Biology, University Hospital of Ioannina, Ioannina, 45110 Greece.
authors.forename: Georgios
authors.initials: G
authors.lastname: Vartholomatos
authors.affiliation: Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece ; Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (IMBB-FORTH), University Campus, Ioannina, 45110 Greece.
authors.forename: Evangelos
authors.initials: E
authors.lastname: Kolettas
authors.affiliation: Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, 45110 Greece.
authors.forename: Theodore
authors.initials: T
authors.lastname: Tzavaras
keywords: Exaptation; Mouse genome; PSF; Retrotransposon; VL30s