Abstract
Long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) might affect transcription regulation of neighboring genes. In our previous study, we showed that the solitary LTR residing in the KIAA1245/NBPF gene subfamily displayed high enhancer activity in a transformed embryonal carcinoma cell line Tera 1. In this study, we performed a functional dissection of the LTR and studied its deletion series. Using transient transfection assay, we confirmed the ability of the LTR to drive the expression of the luciferase reporter gene in Tera1 cells. At the same time, in two other transformed cell lines tested, NGP and NT2/D1, the full-size LTR and its fragments showed no or low enhancer activity, thus demonstrating cell type specificity of the LTR enhancer activity. The functional dissection of the LTR revealed a specific region within the U3 part appeared to be responsible for the enhancer properties. We showed that the identified enhancer was able to work in a highly cell type specific manner. The data obtained are in line with the hypothesis suggesting that KIAA1245/NBPF LTR may affect the transcription regulation of the KIAA1245/NBPF subfamily genes.
Similar content being viewed by others
Abbreviations
- LTR:
-
long terminal repeat
- HERV-K:
-
Human endogenous retrovirus of the K
- NBPF:
-
Neuroblastoma breakpoint family
- NCBI:
-
National Center for Biotechnology Information of the USA
- UCSC:
-
University of California Santa Cruz
References
International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature. 409(6822), 860–921.
Tristem M. 2000. Identification and characterization of novel human endogenous retrovirus families by phylogenetic screening of the human genome mapping project database. J. Virol. 74, 3715–3730.
Gifford R., Tristem M. 2003. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes. 26(3), 291–315.
Abrink M., Larsson E., Hellman L. 1998. Demethylation of ERV3, an endogenous retrovirus regulating the Kruppel-related zinc finger gene H-plk, in several human cell lines arrested during early monocyte development. DNA Cell Biol. 17, 27–37.
Di Cristofano A., Strazullo M., Longo L., La Mantia G. 1995. Characterization and genomic mapping of the ZNF80 locus: Expression of this zinc-finger gene is driven by a solitary LTR of ERV9 endogenous retroviral family. Nucleic Acids Res. 23, 2823–2830.
Calomme C., Dekoninck A., Nizet S., Adam E., Nguyên T.L., van Den Broeke A., Willems L., Kettmann R., Burny A., van Lint C. 2004. Overlapping CRE and E box motifs in the enhancer sequences of the bovine leukemia virus 5′ long terminal repeat are critical for basal and acetylation-dependent transcriptional activity of the viral promoter: implications for viral latency. J. Virol. 78(24), 13848–13864.
Huh J.W., Kim D.S., Kang D.W., Ha H.S., Ahn K., Noh Y.N., Min D.S., Chang K.T., Kim H. S. 2008. Transcriptional regulation of GSDML gene by antisense-oriented HERV-H LTR element. Arch. Virol. 153(6), 1201–1205.
Buzdin A., Kovalskaya-Alexandrova E., Gogvadze E., Sverdlov E. 2006. At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription. J. Virol. 80(21), 10752–10762.
Sverdlov E.D. 1998. Perpetually mobile footprints of ancient infections in human genome. FEBS Lett. 428(1-2), 1–6.
Sverdlov E.D. 2000. Retroviruses and primate evolution. Bioessays. 22, 161–171.
Leib-Mosch C., Haltmeier M., Werner T., Geigl E.M., Brack-Werner R., Francke U., Erfle V., Hehlmann R. 1993. Genomic distribution and transcription of solitary HERV-K LTRs. Genomics. 18, 261–269.
Lower R., Lower J., Kurth R. 1996. The viruses in all of us: Characteristics and biological significance of human endogenous retrovirus sequences. Proc. Natl. Acad. Sci. USA. 93, 5177–5184.
Tonjes R.R., Löwer R., Boller K., Denner J., Hasenmaier B., Kirsch H., König H., Korbmacher C., Limbach C., Lugert R., Phelps RC., Scherer J., Thelen K., Löwer J., Kurth R. 1996. HERV-K: The biologically most active human endogenous retrovirus family. J. AIDS Hum. Retrovirol. 13Suppl 1, S261–S267.
Domansky A.N., Kopantzev E.P., Snezhkov E.V., Lebedev Y.B., Leib-Mosch C., Sverdlov E.D. 2000. Solitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region. FEBS Lett. 472(2–3), 191–195.
Ruda V.M., Akopov S.B., Trubetskoy D.O., Manuylov N.L., Vetchinova A.S., Zavalova L.L., Nikolaev L.G., Sverdlov E.D. 2004. Tissue specificity of enhancer and promoter activities of a HERV-K(HML-2) LTR. Virus Res. 104(1), 11–16.
Domanskii A.N., Akopov S.B., Lebedev Iu.B., Nikolaev L.G., Sverdlov E.D. Enhancer activity of solitary long terminal repeat of the human endogenous retrovirus of the HERV-K family. Bioorg. Khim. 28(4), 341–345.
Schon U., Seifarth W., Baust C., Hohenadl C., Erfle V., Leib-Mosch C. 2001. Cell type-specific expression and promoter activity of human endogenous retroviral long terminal repeats. Virology. 279(1), 280–291.
Medstrand P., Landry J.R., Mager D.L. 2001. Long terminal repeats are used as alternative promoters for the endothelin B receptor and apolipoprotein C-I genes in humans. J. Biol. Chem. 276, 1896–1903.
Vinogradova T.V., Zhulidov P.A., Illarionova A.E., Sverdlov E.D. 2002. A new KIAA1245 gene family with or without HERV-K LTRs in their introns. Bioorg. Khim. 28(4), 346–350.
Vandepoele K., van Roy N., Staes K., Speleman F., van Roy F. 2005. A novel gene family NBPF: Intricate structure generated by gene duplications during primate evolution. Mol. Biol. Evol. 2005. 22(11), 2265–2274.
Illarionova A.E., Vinogradova T.V., Sverdlov E.D. 2007. Only those genes of the KIAA1245 gene subfamily that contain HERV(K) LTRs in their introns are transcriptionally active. Virology. 358(1), 39–47.
Elkahloum A.G., Bittner M., Hoskins K., Gemmill R., Meltzer P.S. 1996. Molecular cytogenetic characterization and physical mapping of 12q13-15 amplification in human cancers. Genes Chromosomes Cancer. 17(4), 205–214.
Maniatis, T., Fritsch, E.F., Sambrook, J. 1982. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Lab. Press.
McGee-Estrada K., Fan H. 2006. In vivo and in vitro analysis of factor binding sites in Jaagsiekte sheep retrovirus long terminal repeat enhancer sequences: Toles of HNF-3, NF-I, and C/EBP for activity in lung epithelial cells. J. Virol. 80(1), 332–341.
McGee-Estrada K., Fan H. 2007. Comparison of LTR enhancer elements in sheep beta retroviruses: Insights into the basis for tissue-specific expression. Virus Genes. 35(2), 303–312.
Ha H.S., Huh J.W., Kim D.S., Kang D.W., Cho B.W., Kim H.S. 2007. Promoter activity of the long terminal repeats of porcine endogenous retroviruses of the Korean domestic pig. Mol. Cells. 24(1), 148–151.
Akopov S.B., Chernov I.P., Vetchinova A.S., Bulanenkova S.S., Nikolaev L.G. 2007. Identification and mapping of cis-regulatory elements within long genomic sequences. Mol. Biol. 41, 717–722.)
Boshart M., Weber F., Jahn G., Dorsch-Häsler K., Fleckenstein B., Schaffner W. 1985. A very strong enhancer is located upstream of an immediate early gene of human cytomegalovirus. Cell. 41(2), 521–530.
Hollon T., Yoshimura F. 1989. Mapping of functional regions of murine retrovirus long terminal repeat enhancers: enhancer domains interact and are not independent in their contributions to enhancer activity. J. Virol. 63(8), 3353–3361.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © N.D. Abrarova, E.A. Stoukacheva, V.V. Pleshkan, T.V. Vinogradova, E.D. Sverdlov, 2010, published in Molekulyarnaya Biologiya, 2010, Vol. 44, No. 4, pp. 627–634.
The article was translated by the authors.
Rights and permissions
About this article
Cite this article
Abrarova, N.D., Stoukacheva, E.A., Pleshkan, V.V. et al. Functional analysis of the HERV-K LTR residing in the KIAA1245/NBPF subfamily genes. Mol Biol 44, 552–558 (2010). https://doi.org/10.1134/S0026893310040084
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0026893310040084