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Determination of L1 retrotransposition kinetics in cultured cells
Open accessAbstract
L1 retrotransposons are autonomous retroelements that are active in the human and mouse genomes. Previously, we developed a cultured cell assay that uses a neomycin phosphotransferase ( neo ) retrotransposition cassette to determine relative retrotransposition frequencies among various L1 elements. Here, we describe a new retrotransposition assay that uses an enhanced green fluorescent protein (EGFP) retrotransposition cassette to determine retrotransposition kinetics in cultured cells. We show that retrotransposition is not detected in cultured cells during the first 48 h post-transfection, but then proceeds at a continuous high rate for at least 16 days. We also determine the relative retrotransposition rates of two similar human L1 retrotransposons, L1(RP)and L1.3. L1(RP)retrotransposed in the EGFP assay at a rate of approximately 0.5% of transfected cells/day, approximately 3-fold higher than the rate measured for L1.3. We conclude that the new assay detects near real time retrotransposition in a single cell and is sufficiently sensitive to differentiate retrotransposition rates among similar L1 elements. The EGFP assay exhibits improved speed and accuracy compared to the previous assay when used to determine relative retrotransposition frequencies. Furthermore, the EGFP cassette has an expanded range of experimental applications.
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“The episomal L1-EGFP reporter plasmid and the L1 5′UTR-Luciferase reporter plasmid used in this study were both described previously25,50.”
From SIRT6 represses LINE1 retrotransposons by ribosylating KAP1 but this repression fails with stress and age (2014) · cites this paper as [25]
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Sorted by citations
Items 101–200 of 291
The tumor suppressor microRNA let-7 inhibits human LINE-1 retrotransposition
Tristán-Ramos, P., Rubio-Roldán, A., Peris, G., Sánchez, L., Amador‐Cubero, S., Viollet, S., Cristofari, G., & Heras, S. R. (2020) · Nature Communications · doi:10.1038/s41467-020-19430-4 · Cited by 72
AID can restrict L1 retrotransposition suggesting a dual role in innate and adaptive immunity
MacDuff, D. A., Demorest, Z. L., & Harris, R. S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp030 · Cited by 65
Pereira, G., Sánchez, L., Schaughency, P., Rubio-Roldán, A., Choi, J. A., Planet, E., Batra, R., Turelli, P., Trono, D., Ostrow, L. W., et al. (2018) · Mobile DNA · doi:10.1186/s13100-018-0138-z · Cited by 70
“EGFP reporter gene can be expressed from its own promoter only after the L1 is transcribed, the γ-globin intron is removed by splicing, the L1-reporter cassette hybrid transcript is reverse-transcribed, and its cDNA inserted in the genome [84, 87].”
BackgroundInfluentialRNase L restricts the mobility of engineered retrotransposons in cultured human cells
Zhang, A., Dong, B., Doucet, A. J., Moldovan, J. B., Moran, J. V., & Silverman, R. H. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1308 · Cited by 68
Pittoggi, C., Beraldi, R., Sciamanna, I., Barberi, L., Giordano, R. C., Magnano, A. R., Torosantucci, L., Pescarmona, E. O., & Spadafora, C. (2006) · Molecular Reproduction and Development · doi:10.1002/mrd.20550 · Cited by 60
“The map in Figure 1A shows that in this construct the EGFP gene is interrupted by a g-globin derived intron, cloned in the opposite orientation relative to the reporter gene (Ostertag et al., 2000).”
LINE-1 Cultured Cell Retrotransposition Assay
Kopera, H. C., Larson, P. A., Moldovan, J. B., Richardson, S. R., Liu, Y., & Moran, J. V. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3372-3_10 · Cited by 63
“The following protocol has been adapted from previously published assays (24, 36, 43, 58, 66) and is optimized for HeLa cells.”
BackgroundMethodMartin, S. L., Bushman, D. M., Wang, F., Li, P. W.-L., Walker, A., Cummiskey, J., Branciforte, D., & Williams, M. C. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn554 · Cited by 58
“Transfected cells were examined daily for the presence of green cells, which indicate retrotransposition of L1 from the transfected plasmid into genomic DNA (20).”
BackgroundL1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution
Nguyen, T. H. M., Carreira, P. E., Sanchez-Luque, F. J., Schauer, S. N., Fagg, A. C., Richardson, S. R., Davies, C. M., Jesuadian, J. S., Kempen, M.-J. H. C., Troskie, R., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.090 · Cited by 60
Extracellular vesicles mediate the horizontal transfer of an active LINE‐1 retrotransposon
Kawamura, Y., Calle, A. S., Yamamoto, Y., Sato, T., & Ochiya, T. (2019) · Journal of Extracellular Vesicles · doi:10.1080/20013078.2019.1643214 · Cited by 56
Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles
Mandal, P. K., Ewing, A. D., Hancks, D. C., & Kazazian, H. H. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt225 · Cited by 54
“First, as a control, we tested whether the epitope tags significantly altered activity by using a well-characterized cell culture retrotransposition assay (43).”
MethodInfluentialLi, P. W.-L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj490 · Cited by 53
The L1 retrotransposition assay: A retrospective and toolkit
Rangwala, S. M. (2009) · Methods · doi:10.1016/j.ymeth.2009.04.012 · Cited by 54
Retrotransposons, reverse transcriptase and the genesis of new genetic information
Sciamanna, I., Vitullo, P., Curatolo, A., & Spadafora, C. (2009) · Gene · doi:10.1016/j.gene.2009.07.011 · Cited by 52
Chen, Y., Luo, S., Hu, Y., Mao, B., Wang, X., Lu, Z., Shan, Q., Zhang, J., Wang, S., Feng, G., et al. (2024) · Cell · doi:10.1016/j.cell.2024.06.020 · Cited by 50
“Identifying R2 systems with retrotransposition activity in human cells Next, we used a classic GFP-intron reporter 27,28 to evaluate R2 retrotransposition activity (Figures 2A and 2B).”
The SAMHD1-mediated block of LINE-1 retroelements is regulated by phosphorylation
Herrmann, A., Wittmann, S., Thomas, D., Shepard, C., Kim, B., Ferreirós, N., & Gramberg, T. (2018) · Mobile DNA · doi:10.1186/s13100-018-0116-5 · Cited by 59
“surrogate marker for successful retrotransposition [39].”
The epigenetic regulator PLZF represses L1 retrotransposition in germ and progenitor cells
Puszyk, W. M., Down, T. A., Grimwade, D. J., Chomienne, C., Oakey, R. J., Solomon, E., & Guidez, F. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.118 · Cited by 53
Zhen, Z., Chen, Y., Wang, H., Tang, H., Zhang, H., Liu, H., Jiang, Y., & Mao, Z. (2023) · Nature Communications · doi:10.1038/s41467-023-43001-y · Cited by 52
“…DNA damage induced cGAS-mediated ORF2p degradation and L1 retrotransposition inhibition, raised by Reviewer #2, we found that HeLa cells treated with etoposide actually entered a state of senescence, evidenced by upregulation of p21, an increase in the positive rate of β-gal staining, and…”
Ge, L., Jin, X., Ma, D., Wang, Z.-Y., Liu, C., Zhou, C., Zhao, S., Yu, T., Liu, X., Di, G. H., et al. (2024) · Cell Research · doi:10.1038/s41422-023-00909-w · Cited by 51
The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology
Chesnokova, E., Beletskiy, A., & Kolosov, P. M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23105847 · Cited by 51
Long interspersed nuclear element-1 expression and retrotransposition in prostate cancer cells
Briggs, E. M., Ha, S., Mita, P., Brittingham, G. P., Sciamanna, I., Spadafora, C., & Logan, S. K. (2018) · Mobile DNA · doi:10.1186/s13100-017-0106-z · Cited by 45
“Functional GFP is only expressed after retrotransposition [8, 29, 30].”
Transposable elements in brain health and disease
Ahmadi, A., Toma, I. D., Vilor‐Tejedor, N., Ghamsari, M. R. E., & Sadeghi, I. (2020) · Ageing Research Reviews · doi:10.1016/j.arr.2020.101153 · Cited by 49
Kirilyuk, A., Tolstonog, G. V., Damert, A., Held, U., Hahn, S., Löwer, R., Buschmann, C., Horn, A. V., Traub, P., & Schumann, G. G. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1045 · Cited by 46
Ciaudo, C., Jay, F., Okamoto, I., Chen, C., Sarazin, A., Servant, N., Barillot, E., Heard, É., & Voinnet, O. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003791 · Cited by 46
“gain-of-GFP retrotransposition assay previously developed by Prak and colleagues [30] and validated in WT mESCs [31].”
MethodRetractedMiyoshi, T., Makino, T., & Moran, J. V. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.018 · Cited by 51
“A3A-mediated C-to-U deamination events were only modestly decreased in the LEAP oligonucleotide adapter in either the presence or absence of RNase H when RPA was included in the LEAP reaction (Figures 6C and 6D), which could be due to the small size of the LEAP oligonucleotide adapter (58 nucleotides) or lower RPA/sub…”
MethodInfluentialPathogenic orphan transduction created by a nonreference LINE-1 retrotransposon
Sólyom, S., Ewing, A. D., Hancks, D. C., Takeshima, Y., Awano, H., Matsuo, M., & Kazazian, H. H. (2011) · Human Mutation · doi:10.1002/humu.21663 · Cited by 43
“This cassette was designed so that translation of the EGFP reporter gene occurs only after LINE-1 reverse transcription and integration of its cDNA copy into the genome—that is, after a retrotransposition event [Moran et al., 1996; Ostertag et al., 2000].”
MethodChang, Y., Keegan, R. M., Prazak, L., & Dubnau, J. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000278 · Cited by 40
Banuelos‐Sanchez, G., Sánchez, L., Benitez‐Guijarro, M., Sanchez-Carnerero, V., Salvador‐Palomeque, C., Tristán-Ramos, P., Benkaddour-Boumzaouad, M., Morell, S., García-Puche, J. L., Heras, S. R., et al. (2019) · Cell chemical biology · doi:10.1016/j.chembiol.2019.04.010 · Cited by 48
Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective
Betancourt, A. J., Wei, K. H.-C., Huang, Y., & Lee, Y. C. G. (2024) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120822-105708 · Cited by 46
Stable Integration of Transgenes Delivered by a Retrotransposon–Adenovirus Hybrid Vector
Soifer, H. S., Higo, C., Kazazian, H. H., Moran, J. V., Mitani, K., & Kasahara, N. (2001) · Human Gene Therapy · doi:10.1089/104303401750298571 · Cited by 42
“3 element can continue to retrotranspose at a rate of about 0.1% of transfected cells per day when expressed from a self-replicating plasmid (Ostertag et al. , 2000) in hygromycin-selected cells.”
InfluentialLiang, W., Xu, J.-W., Yuan, W., Song, X., Zhang, J., Wei, W., Yu, X.-F., & Yang, Y. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157220 · Cited by 44
Specific localization of transcription factors in the chromatin of mouse mature spermatozoa
Pittoggi, C., Magnano, A. R., Sciamanna, I., Giordano, R. C., Lorenzini, R., & Spadafora, C. (2001) · Molecular Reproduction and Development · doi:10.1002/mrd.1066 · Cited by 40
“Recent evidence further support the view that retrotransposal integration events can modify the genome structure by transducing DNA sequences to new genomic locations (Moran et al., 1999; Ostertag et al., 2000).”
BackgroundA Reverse Transcriptase-Dependent Mechanism Plays Central Roles in Fundamental Biological Processes
Spadafora, C. (2008) · Systems Biology in Reproductive Medicine · doi:10.1080/19396360701876815 · Cited by 39
“We therefore incubated spermatozoa with a DNA plasmid containing a ‘‘retrotransposition cassette’’ of an EGFP reporter gene interrupted by an intron sequence in the opposite orientation [Ostertag et al. 2000].”
MethodDifferential Sensitivities of Retroviruses to Integrase Strand Transfer Inhibitors
Koh, Y., Matreyek, K. A., & Engelman, A. (2011) · Journal of Virology · doi:10.1128/jvi.02541-10 · Cited by 37
“2 g of LINE-1 bearing L1RP-EGFP(puro) or negative control pL1RP(JM111)EGFP(puro) were also scored after 7 days, with the addition of puromycin (2 g/ml) at 48 h posttransfection to enhance the selection of de novo events (33).”
MethodHuman TRIM5α senses and restricts LINE-1 elements
Volkmann, B., Wittmann, S., Lagisquet, J., Deutschmann, J., Eissmann, K., Ross, J. J., Biesinger, B., & Gramberg, T. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1922366117 · Cited by 41
“We tested the ability of the different TRIM proteins to restrict LINE-1 elements using a well-established reporter assay (34).”
MethodCondensation of LINE-1 is critical for retrotransposition
Sil, S., Keegan, S., Ettefa, F., Denes, L. T., Boeke, J. D., & Holt, L. J. (2023) · eLife · doi:10.7554/elife.82991 · Cited by 39
Dicer, a new regulator of pluripotency exit and LINE ‐1 elements in mouse embryonic stem cells
Bodak, M., Cirera‐Salinas, D., Yu, J., Ngondo, R. P., & Ciaudo, C. (2016) · FEBS Open Bio · doi:10.1002/2211-5463.12174 · Cited by 37
More active human L1 retrotransposons produce longer insertions
Farley, A. H. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh202 · Cited by 36
“Transfection and selection of HeLa cells containing neomycin-tagged L1 constructs (L1-mneoI) were carried out as described previously (6,35).”
MethodLINE-1 retrotransposons contribute to mouse PV interneuron development
Bodea, G. O., Botto, J. M., Ferreiro, M. E., Sanchez-Luque, F. J., Barreda, J. D. L. R., Rasmussen, J., Rahman, M. A., Fenlon, L. R., Jansz, N., Gubert, C., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01650-2 · Cited by 43
“Cultured cell L1 retrotransposition reporter assay L1 retrotransposition efficiency was measured via an EGFP L1 reporter system in cultured HeLa and PA-1 cells, as described previously 13,17,53 .”
Inhibition of LINE-1 and Alu retrotransposition by exosomes encapsidating APOBEC3G and APOBEC3F
Khatua, A. K., Taylor, H. E., Hildreth, J. E. K., & Popik, W. (2010) · Virology · doi:10.1016/j.virol.2010.01.021 · Cited by 37
“…expressing A3G or other A3 proteins show inhibitory activity against retroelements, we analyzed the effect of isolated exosomes on L1 retrotransposition using an established 293T cell culture-based retrotransposition reporter assay (Brouha et al., 2003; Ostertag et al., 2000; Wei et al., 2000).”
MethodThe Influence of LINE-1 and SINE Retrotransposons on Mammalian Genomes
Richardson, S. R., Doucet, A. J., Kopera, H. C., Moldovan, J. B., Garcia-Perez, J. L., & Moran, J. V. (2015) · ASM Press eBooks · doi:10.1128/9781555819217.ch51 · Cited by 38
Luqman-Fatah, A., Watanabe, Y., Uno, K., Ishikawa, F., Moran, J. V., & Miyoshi, T. (2023) · Nature Communications · doi:10.1038/s41467-022-35757-6 · Cited by 46
Characterization of pre-insertion loci of de novo L1 insertions
Gasior, S. L., Preston, G. J., Hedges, D. J., Gilbert, N., Moran, J. V., & Deininger, P. L. (2006) · Gene · doi:10.1016/j.gene.2006.08.024 · Cited by 34
“Indeed, silencing of L1 selection cassettes has been observed in vitro (Muotri et al., 2005; Ostertag et al., 2000).”
BackgroundSur, D., Kustwar, R. K., Budania, S., Mahadevan, A., Hancks, D. C., Yadav, V., Shankar, S. K., & Mandal, P. K. (2017) · Mobile DNA · doi:10.1186/s13100-017-0101-4 · Cited by 34
“[2], which involved insertion analysis of transgenic mice carrying an engineered L1 that upon retrotransposition expresses green fluorescent protein (GFP) [46], unexpectedly identified retrotransposition-competent cells in many”
Conditional activation of a single‐copy L1 transgene in mice by Cre
An, W., Han, J. S., Schrum, C. M., Maitra, A., Köentgen, F., & Boeke, J. D. (2008) · genesis · doi:10.1002/dvg.20407 · Cited by 30
Schmitt, K. P., Guo, K., Algaier, M., Ruiz, A. J., Cheng, F., Qiu, J., Wissing, S., Santiago, M. L., & Stephens, E. B. (2011) · Virology · doi:10.1016/j.virol.2011.07.017 · Cited by 31
“The engineered L1 enhanced green fluorescent protein (EGFP) reporter (Ostertag et al., 2000) was cloned into the pLRE3-EF1-mEGFPI, which contains a retrotransposition”
MethodThe Minimal Active Human SVA Retrotransposon Requires Only the 5′-Hexamer and Alu-Like Domains
Hancks, D. C., Mandal, P. K., Cheung, L. E., & Kazazian, H. H. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.00860-12 · Cited by 34
“In cell culture, engineered SVA elements, marked with reporter genes (mneoI [26, 61] or mEGFP [66]) also referred to as retrotransposition indicator cassettes, retrotranspose when cotransfected with plasmids expressing L1 proteins (trans-complementation assays).”
BackgroundStructural variant identification and characterization
Balachandran, P., & Beck, C. R. (2020) · Chromosome Research · doi:10.1007/s10577-019-09623-z · Cited by 37
APE-type non-LTR retrotransposons: determinants involved in target site recognition
Zingler, N., Weichenrieder, O., & Schumann, G. G. (2005) · Cytogenetic and Genome Research · doi:10.1159/000084959 · Cited by 31
“…Since tagged L1 elements retrotranspose in HeLa cells quite efficiently, but do not do so in other tested human cell lines (Moran et al., 1996; Ostertag et al., 2000; Ostertag and Kazazian, 2001), it was concluded that HeLa cells express host factors that are essential for L1…”
BackgroundRetrotransposons Influence the Mouse Transcriptome: Implication for the Divergence of Genetic Traits
Horie, K., Saito, E.-S., Keng, V. W., Ikeda, R., Ishihara, H., & Takeda, J. (2007) · Genetics · doi:10.1534/genetics.107.071647 · Cited by 33
HIV-1 Vpr and p21 restrict LINE-1 mobility
Kawano, K., Doucet, A. J., Ueno, M., Kariya, R., An, W., Marzetta, F., Kuroki, M., Turelli, P., Sukegawa, S., Okada, S., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky688 · Cited by 28
“The EGFP-based retrotransposition assay was performed as followed: 293T cells were seeded in 12-well plates at 5 × 104 cells per plate and transfected the next day using FuGENE6 with 500 ng of either an EGFP-based retrotransposition reporter pL1RP-EGFP (54) or its corresponding negative control pL1RP(JM111)-EGFP which…”
BackgroundMethodInfluentialLavasanifar, A., Sharp, C. N., Korte, E. A., Yin, T., Hosseinnejad, K., & Jortani, S. A. (2019) · Clinica Chimica Acta · doi:10.1016/j.cca.2019.02.015 · Cited by 29
Conservation and Innovation of APOBEC3A Restriction Functions during Primate Evolution
McLaughlin, R. N., Gable, J. T., Wittkopp, C. J., Emerman, M., & Malik, H. S. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw070 · Cited by 26
“LINE-1 plasmids were a gift from John Moran, JM101 99_gfp_LRE3_puro and JM111 99_gfp_LRE3_puro (ORF1 mutant) (Moran et al. 1996; Ostertag et al. 2000) and Wenfang An, pYX016 (CAG promoter—mouse ORFeus—Fluc—globin intron with renilla luciferase constitutive expression from the same plasmid) and…”
InfluentialThe impact of transposable element activity on therapeutically relevant human stem cells
Schumann, G. G., Fuchs, N. V., Tristán-Ramos, P., Sebe, A., Ivics, Z., & Heras, S. R. (2019) · Mobile DNA · doi:10.1186/s13100-019-0151-x · Cited by 28
In Vitro Screening for Compounds That Enhance Human L1 Mobilization
Terasaki, N., Goodier, J. L., Cheung, L. E., Wang, Y. J., Kajikawa, M., Kazazian, H. H., & Okada, N. (2013) · PLoS ONE · doi:10.1371/journal.pone.0074629 · Cited by 28
“Testing initially for efficacy in 6-well plates, we cotransfected 99-PUR-RPS-mGLucI with empty vector or cDNA constructs whose protein products were previously determined to alter EGFP-reporter retrotransposition in HEK293T cell culture (Fig.”
BackgroundMethodInfluentialValle, F. D., Thimma, M., Caiazzo, M., Pulcrano, S., Celii, M., Adroub, S. A., Liu, P., Alanis‐Lobato, G., Broccoli, V., & Orlando, V. (2020) · Stem Cell Reports · doi:10.1016/j.stemcr.2019.12.002 · Cited by 26
“Finally, to prove that transdifferentiating post-mitotic cells are compatible and support the retrotranspositionmachinery, we overexpressed two different exogenous mouse L1 element (pGF21 and pTN201 plasmids inwild-typeMEF cells, which were generously provided by Prof. John Goodier) with an antisense oriented neomycin…”
BackgroundMethodInfluentialGerdes, P., Lim, S. M., Ewing, A. D., Larcombe, M. R., Chan, D. L.-K., Sanchez-Luque, F. J., Walker, L., Carleton, A. L., James, C., Knaupp, A. S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35180-x · Cited by 24
Zhang, P., Ludwig, A. K., Hastert, F. D., Rausch, C., Lehmkuhl, A., Hellmann, I., Smets, M., Leonhardt, H., & Cardoso, M. C. (2017) · Nucleus · doi:10.1080/19491034.2017.1330238 · Cited by 25
“This fits well the previously reported L1 de novo retrotransposition kinetics.(38) To further validate the increase of L1 retrotransposition induced by Tet1CD, we used flow cytometry analysis.”
MethodDynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation
Salvador‐Palomeque, C., Sanchez-Luque, F. J., Fortuna, P. R. J., Ewing, A. D., Wolvetang, E. J., Richardson, S. R., & Faulkner, G. J. (2019) · Molecular and Cellular Biology · doi:10.1128/mcb.00499-18 · Cited by 28
Adney, E. M., Ochmann, M. T., Sil, S., Truong, D. M., Mita, P., Wang, X., Kahler, D. J., Fenyö, D., Holt, L. J., & Boeke, J. D. (2019) · Genetics · doi:10.1534/genetics.119.302601 · Cited by 27
The Rhox gene cluster suppresses germline LINE1 transposition
Tan, K., Kim, M. E., Song, H.-W., Skarbrevik, D., Babajanian, E., Bedrosian, T. A., Gage, F. H., & Wilkinson, M. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2024785118 · Cited by 23
“We generated a RHOXF2-small hairpin (sh)RNA lentivirus to knockdown RHOXF2 in a K562 L1-GFP reporter line that harbors an EGFP transposition cassette inserted into the 3′ untranslated region of a LINE1 element to assay LINE1 transposition (59).”
MethodCondensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells
Ward, J. R., Vasu, K., Deutschman, E., Halawani, D., Larson, P. A., Zhang, D., Willard, B. B., Fox, P. L., Moran, J. V., & Longworth, M. S. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1007051 · Cited by 26
L1 retrotransposon-mediated stable gene silencing
Yang, N. (2005) · Nucleic Acids Research · doi:10.1093/nar/gni056 · Cited by 24
“Since our RNAi system is based on L1 retrotransposition, we further characterized its properties in human cells, using a GFP-cassette to replace the neo-cassette for retrotransposition detection (24).”
MethodBona, N., & Crossan, G. P. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01067-8 · Cited by 23
LINE-1 Retroelements Complexed and Inhibited by Activation Induced Cytidine Deaminase
Metzner, M., Jäck, H., & Wabl, M. R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0049358 · Cited by 24
“, and described in [24]), with two missense mutations in the ORF1 (and thus nonfunctional) served as a negative control.”
BackgroundMethodInfluentialTanaka, A., Nakatani, Y., Hamada, N., Jinno‐Oue, A., Shimizu, N., Wada, S., Funayama, T., Mori, T., Islam, S., Hoque, S. A., et al. (2012) · Mutagenesis · doi:10.1093/mutage/ges025 · Cited by 23
Long INterspersed element‐1 mobility as a sensor of environmental stresses
Re, B. D., & Giorgi, G. (2020) · Environmental and Molecular Mutagenesis · doi:10.1002/em.22366 · Cited by 25
“Enhanced green fluorescent protein (EGFP) reporter gene (mEGFPI) allowed for reduced assay times (about 7 days) because reporter gene expression could be detected by flow cytometry analysis and/or fluorescence microscopy observation (Ostertag et al., 2000).”
BackgroundThe DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive‐strand RNA viruses
Bonaventure, B., Rebendenne, A., Valadão, A. L. C., Arnaud‐Arnould, M., Gracias, S., García-de-Gracia, F., McKellar, J., Labaronne, E., Tauziet, M., Vivet‐Boudou, V., et al. (2022) · EMBO Reports · doi:10.15252/embr.202154061 · Cited by 20
Karimi, A., Madjd, Z., Habibi, L., & Akrami, S. M. (2014) · Toxicology Letters · doi:10.1016/j.toxlet.2014.05.025 · Cited by 21
“To evaluate the effect of arsenic on L1 retrotransposition, the in vitro retrotransposition assay was used as described (Ostertag et al., 2000).”
MethodMutagenesis in rodents using the L1 retrotransposon
Ostertag, E. M., Madison, B., & Kano, H. (2007) · Genome biology · doi:10.1186/gb-2007-8-s1-s16 · Cited by 21
“In one transgenic model, a highly active human L1 element (L1RP) [41], which was tagged with an EGFP retrotransposition cassette [42] and was transcribed using its endogenous promoter, exhibited somatic retrotransposition within neuronal precursors [40].”
BackgroundSelf-citationLuca, C. D., Gupta, A. K., & Bortvin, A. L. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010797 · Cited by 25
Heritable L1 Retrotransposition Events During Development: Understanding Their Origins
Richardson, S. R., & Faulkner, G. J. (2018) · BioEssays · doi:10.1002/bies.201700189 · Cited by 20
SV40 Large T Antigen Up-regulates the Retrotransposition Frequency of Viral-like 30 Elements
Noutsopoulos, D., Vartholomatos, G., Kolaitis, N., & Tzavaras, T. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.06.030 · Cited by 20
Lazaros, L. A., Kitsou, C., Kostoulas, C., Bellou, S., Hatzi, E. G., Ladias, P., Stefos, Τ., Markoula, S., Galani, V., Vartholomatos, G., et al. (2017) · Fertility and Sterility · doi:10.1016/j.fertnstert.2016.12.027 · Cited by 20
Zamane, S. A., Nobel, F. A., Jebin, R. A., Amin, M. A., Somadder, P. D., Antora, N. J., Hossain, M. I., Islam, M. J., Ahmed, K., & Moni, M. A. (2021) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2021.100781 · Cited by 21
Reviving the Dead: History and Reactivation of an Extinct L1
Yang, L., Brunsfeld, J., Scott, L., & Wichman, H. A. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004395 · Cited by 19
“An independent human L1 construct, pWA192 [67], was used as a positive control and an ORF1 mutant of L1rp [68] that blocks retrotransposition was used as a negative control.”
MethodHepatitis C virus infection restricts human LINE-1 retrotransposition in hepatoma cells
Schöbel, A., Nguyen-Dinh, V., Schumann, G. G., & Herker, E. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009496 · Cited by 19
Evaluating the Extent of LINE-1 Mobility Following Exposure to Heavy Metals in HepG2 Cells
Karimi, A., Madjd, Z., Habibi, L., & Akrami, S. M. (2014) · Biological Trace Element Research · doi:10.1007/s12011-014-0015-7 · Cited by 19
“retrotransposition assay system [28].”
Kannan, M., Li, J., Fritz, S. E., Husarek, K. E., Sanford, J. C., Sullivan, T. L., Tiwary, P. K., An, W., Boeke, J. D., & Symer, D. E. (2017) · Mobile DNA · doi:10.1186/s13100-017-0091-2 · Cited by 19
“Instead, linear amplification mediatedPCR (LAM-PCR) was performed to recover any new L1 ORFeus integrants, regardless of their expression of GFPuv.”
MethodInfluentialp53-mediated regulation of LINE1 retrotransposon-derived R-loops
Paul, P., Kumar, A., De, A. K., Parida, A. S., Bhadke, G., Khatua, S., Pattanayak, F., & Tiwari, B. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.108200 · Cited by 20
“…to determine whether p53 also enables resilencing of retrotransposition activation, we used a synthetic L1 designated 99-gfp-LRE3 retrotransposition indicator (46, 47), using HDACi treatment, similar experiment was conducted on stably transfected parental WT and p53 − / − A375 and U2OS cells, ).”
Spliced integrated retrotransposed element (SpIRE) formation in the human genome
Larson, P. A., Moldovan, J. B., Jasti, N., Kidd, J. M., Beck, C. R., & Moran, J. V. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2003067 · Cited by 20
Angileri, K. M., & Gross, J. M. (2020) · Scientific Reports · doi:10.1038/s41598-020-68016-z · Cited by 16
Noutsopoulos, D., Markopoulos, G. S., Koliou, M., Dova, L., Vartholomatos, G., Kolettas, E., & Tzavaras, T. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.09.012 · Cited by 16
Renner, T. M., Bélanger, K., Goodwin, L. R., Campbell, M., & Langlois, M. (2018) · Virology · doi:10.1016/j.virol.2018.05.015 · Cited by 16
Re, B. D., Marcantonio, P., Gavoçi, E., Bersani, F., & Giorgi, G. (2012) · Mutation Research/Genetic Toxicology and Environmental Mutagenesis · doi:10.1016/j.mrgentox.2012.07.004 · Cited by 14
Five months of voluntary wheel running downregulates skeletal muscle LINE-1 gene expression in rats
Romero, M. A., Mumford, P. W., Roberson, P. A., Osburn, S. C., Parry, H. A., Kavazis, A. N., Gladden, L. B., Schwartz, T. S., Baker, B. A., Toedebusch, R. G., et al. (2019) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00301.2019 · Cited by 12
“For example, there is evidence that the DNA binding domain of the DNA transposon Tc1/mariner has been co-opted by animals in the PAX3 gene, which is important for skeletal muscle development (27, 50).”
BackgroundRe, B. D., Marcantonio, P., Capri, M., & Giorgi, G. (2010) · Experimental Cell Research · doi:10.1016/j.yexcr.2010.06.024 · Cited by 14
Markopoulos, G. S., Noutsopoulos, D., Mantziou, S., Vartholomatos, G., Monokrousos, N., Angelidis, C. E., & Tzavaras, T. (2013) · Toxicological Sciences · doi:10.1093/toxsci/kft118 · Cited by 13
Tracing Mobile DNAs: From Molecular to Population Scales
Fan, W., Wang, L., Chu, J., Li, H., Kim, E. Y., & Cho, J. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.837378 · Cited by 12
L1 Retrotransposition in Neural Progenitor Cells
Muotri, A. R. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-3372-3_11 · Cited by 13
Kawashima, T., Osanai, M., Futahashi, R., Kojima, T., & Fujiwara, H. (2007) · Virus Research · doi:10.1016/j.virusres.2007.03.014 · Cited by 12
Somatic retrotransposition in the developing rhesus macaque brainPreprint
Billon, V., Sanchez-Luque, F. J., Rasmussen, J., Bodea, G. O., Gerhardt, D. J., Gerdes, P., Cheetham, S. W., Schauer, S. N., Ajjikuttira, P., Meyer, T. J., et al. (2022) · Genome Research · doi:10.1101/gr.276451.121 · Cited by 12
“The resulting fragment was digested with NotI and SwaI restriction enzymes and cloned into the NotI and BstZ17I sites of the three aforementioned original vectors lacking the human L1 3 ′ UTR downstream from the BstZ17I site (Moran et al. 1996; Ostertag et al. 2000).”
InfluentialPlug and play modular strategies for synthetic retrotransposons
An, W. (2009) · Methods · doi:10.1016/j.ymeth.2009.05.013 · Cited by 11
Habibi, L., Shokrgozar, M. A., Motamedi, M., & Akrami, S. M. (1996) · Europe PMC (PubMed Central) · doi:10.6091/ibj.1230.2013 · Cited by 13
“To confirm L1-RP GFPtagged knocked-in clones, PCR was performed for the GFP gene using forward (5′ GCACCATCTTCTTCAA GGACGAC-3) and reverse primers (5′-TCTTTGC TCAGGGCGGACTG-3) [23] with the following protocol: 250 ng DNA (from C1-C5 cells), 300 nM final concentration for forward and reverse primers and 10 µl PCR 2× ma…”
BackgroundMethodInfluentialProstate-specific loss of UXT promotes cancer progression
Wang, Y., Schafler, E. D., Thomas, P. A., Ha, S., David, G., Adney, E. M., Garabedian, M. J., Lee, P., & Logan, S. K. (2019) · Oncotarget · doi:10.18632/oncotarget.26573 · Cited by 11
“To test this, we conducted retrotransposition assays using a Neo-AI-based retrotransposition reporter [28].”
MethodThe Potential Regulation of L1 Mobility by RNA Interference
Horman, S. R., Svoboda, P., & Prak, E. T. L. (2006) · BioMed Research International · doi:10.1155/jbb/2006/32713 · Cited by 10
“The standard L1 reporter construct used in our laboratory (L1-EGFP) consists of the CMV promoter, the human L1RP element, and the antisense EGFP gene cloned into the L1 3′UTR followed by the SV40 late poly-A sequence in pCEP4 (construct described in more detail in [51]).”
MethodA yeast model for target-primed (non-LTR) retrotransposition
Goodwin, T. J. D., Busby, J. N., & Poulter, R. T. M. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-263 · Cited by 11
“By studying the effects of various mutations within the L1 sequence, and by analysing the structures of numerous retrotransposed copies, much has been learned about the L1 retrotransposition process and the effect this has on the host genome [[14,21,30-37]; reviewed in ref.”
BackgroundYan, J., Zhao, Y., Du, J., Wang, Y., Wang, S., Wang, Q., Zhao, X., Xu, W., & Zhao, K. (2022) · Mobile DNA · doi:10.1186/s13100-022-00268-0 · Cited by 13
“The retrotransposition-competent vector 99 PUR RPS EGFP (L1-RPS) (22), the retrotransposition incompetent 99 PUR JM111 EGFP (JM111) (22), pc-L1-1FH (L1-1FH) (24), pGL3.”
BackgroundMethodZCCHC3 is a stress granule zinc knuckle protein that strongly suppresses LINE-1 retrotransposition
Goodier, J. L., Wan, H., Soares, A. O., Sánchez, L., Selser, J. M., Pereira, G., Karma, S., Garcia-Perez, J. L., Kazazian, H. H., & García-Cañadas, M. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010795 · Cited by 11
“previously described: 99-PUR-RPS-EGFP, 99-PUR-JM111-RPS-EGFP [45], pc-L1-1FH, pcL1-RP [28], ORF1-EGFP-L1-RP [62], and ZAP-L-FL [29].”
BackgroundMethodInfluentialRangasamy, D. (2010) · Epigenetics · doi:10.4161/epi.5.7.12647 · Cited by 10
“The retrotransposition assay and the determination of retrotransposition frequency were performed as previously described.(23) The numbers of retrotransposed EGFP-positive and -negative cells were determined by flow sorting with a FACSVantage DiVa cell sorter (Becton-Dickinson).”
MethodInfluentialH2O2 signals via iron induction of VL30 retrotransposition correlated with cytotoxicity
Konisti, S., Mantziou, S., Markopoulos, G. S., Thrasyvoulou, S., Vartholomatos, G., Sainis, I., Kolettas, E., Noutsopoulos, D., & Tzavaras, T. (2012) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2012.03.021 · Cited by 10
“In short, assay cells are NIH3T3 cells that (a) express a human antiapoptotic Bcl-2 protein, being resistant to ROSmediated cytotoxic effects, and (b) harbor a VL30 recombinant pNVL-3/EGFP-INT carrying a truncated NVL-3/9 VL30 element tagged with an EGFP-retrotransposition cassette [45].”
Background
Metadata
- Authors
- Ostertag, E. M.
- Affiliations
- University of Pennsylvania (US)
- Corresponding author
- Ostertag, E. M.
- ORCID
- Ostertag, E. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2000-03-15
- Volume
- 28
- Issue
- 6
- Pages
- 1418-1423
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC111040
- OpenAlex
- W2150649207
- Cited by
- 291
- References
- 29
- Citations by year
- 2026: 8 · 2025: 16 · 2024: 10 · 2023: 9 · 2022: 16 · 2021: 12 · 2020: 15 · 2019: 17 · 2018: 14 · 2017: 21 · 2016: 11 · 2015: 9 · 2014: 7 · 2013: 17 · 2012: 9
- FWCI
- 8.97
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- University of Pennsylvania
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- LINE-1 retrotransposons, cultured cells, transposable elements
- MeSH terms
- Cinnamates, Drug Resistance, False Positive Reactions, Globins, HeLa Cells, Humans, Hygromycin B, Introns, Kinetics, Luminescent Proteins, Microscopy, Fluorescence, Puromycin, Recombination, Genetic, RNA Splicing, Sensitivity and Specificity, Time Factors, Transfection, Mutagenesis, Insertional, Genes, Reporter, Retroelements, 3' Untranslated Regions, Green Fluorescent Proteins
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