Characterization of a synthetic human LINE-1 retrotransposon ORFeus-Hs
Open accessAbstract
Long interspersed elements, type 1(LINE-1, L1) are the most abundant and only active autonomous retrotransposons in the human genome. Native L1 elements are inefficiently expressed because of a transcription elongation defect thought to be caused by high adenosine content in L1 sequences. Previously, we constructed a highly active synthetic mouse L1 element (ORFeus-Mm), partially by reducing the nucleotide composition bias. As a result, the transcript abundance of ORFeus-Mm was greatly increased, and its retrotransposition frequency was > 200-fold higher than its native counterpart. In this paper, we report a synthetic human L1 element (ORFeus-Hs) synthesized using a similar strategy. The adenosine content of the L1 open reading frames (ORFs) was reduced from 40% to 27% by changing 25% of the bases in the ORFs, without altering the amino acid sequence. By studying a series of native/synthetic chimeric elements, we observed increased levels of full-length L1 RNA and ORF1 protein and retrotransposition frequency, mostly proportional to increased fraction of synthetic sequence. Overall, the fully synthetic ORFeus-Hs has > 40-fold more RNA but is at most only ~threefold more active than its native counterpart (L1 RP); however, its absolute retrotransposition activity is similar to ORFeus-Mm. Owing to the elevated expression of the L1 RNA/protein and its high retrotransposition ability, ORFeus-Hs and its chimeric derivatives will be useful tools for mechanistic L1 studies and mammalian genome manipulation.
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The absolute average retrotransposition frequency for pLD143 was 4.1%, matching published values.
“The absolute average retrotransposition frequency (percentage of GFP-positive cells) was 4.1, which matches the published values for the reporter used (pLD143)53.”
From L1 drives IFN in senescent cells and promotes age-associated inflammation (2019) · cites this paper as [53]
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Cites
The Human LINE-1 Retrotransposon Creates DNA Double-strand Breaks
Gasior, S. L., Wakeman, T. P., Xu, B., & Deininger, P. L. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.01.089 · Cited by 519 · see citing works
Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes
Han, J. S., Szak, S. T., & Boeke, J. D. (2004) · Nature · doi:10.1038/nature02536 · Cited by 484 · see citing works
Self-citationDetermination of L1 retrotransposition kinetics in cultured cells
Ostertag, E. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.6.1418 · Cited by 291 · see citing works
Human LINE-1 retrotransposon induces DNA damage and apoptosis in cancer cells
Belgnaoui, S. M., Gosden, R. G., Semmes, O. J., & Haoudi, A. (2006) · Cancer Cell International · doi:10.1186/1475-2867-6-13 · Cited by 219 · see citing works
Li, P. W.-L. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj490 · Cited by 53 · see citing works
Flagged first, then by citations
Research works printed but not linked: 27
- Moran JV Holmes SE Naas TP DeBerardinis RJ Boeke JD Kazazian HH Jr High frequency retrotransposition in cultured mammalian cells Cell 1996 87 917 927 10.1016/S0092-8674(00)81998-4 8945518 · DOI · Paper page
- Dewannieux M Esnault C Heidmann T LINE-mediated retrotransposition of marked Alu sequences Nat Genet 2003 35 41 48 10.1038/ng1223 12897783 · DOI
- Dombroski BA Mathias SL Nanthakumar E Scott AF Kazazian HH Jr Isolation of an active human transposable element Science 1991 254 1805 1808 10.1126/science.1662412 1662412 · DOI
- Fanning TG Size and structure of the highly repetitive BAM HI element in mice Nucleic Acids Res 1983 11 5073 5091 10.1093/nar/11.15.5073 6308571 PMC326238 · DOI
- Fanning TG Singer MF LINE-1: a mammalian transposable element Biochim Biophys Acta 1987 910 203 212 2445384
- Grimaldi G Skowronski J Singer MF Defining the beginning and end of KpnI family segments EMBO J 1984 3 1753 1759 6090124 PMC557592
- Loeb DD Padgett RW Hardies SC Shehee WR Comer MB Edgell MH Hutchison CA The sequence of a large L1Md element reveals a tandemly repeated 5' end and several features found in retrotransposons Mol Cell Biol 1986 6 168 182 3023821 PMC367496
- Scott AF Schmeckpeper BJ Abdelrazik M Comey CT O'Hara B Rossiter JP Cooley T Heath P Smith KD Margolet L Origin of the human L1 elements: proposed progenitor genes deduced from a consensus DNA sequence Genomics 1987 1 113 125 10.1016/0888-7543(87)90003-6 3692483 PMC7135745 · DOI
- Hohjoh H Singer MF Sequence-specific single-strand RNA binding protein encoded by the human LINE-1 retrotransposon EMBO J 1997 16 6034 6043 10.1093/emboj/16.19.6034 9312060 PMC1170233 · DOI
- Kolosha VO Martin SL In vitro properties of the first ORF protein from mouse LINE-1 support its role in ribonucleoprotein particle formation during retrotransposition Proc Natl Acad Sci USA 1997 94 10155 10160 10.1073/pnas.94.19.10155 9294179 PMC23331 · DOI
- Kolosha VO Martin SL High-affinity, non-sequence-specific RNA binding by the open reading frame 1 (ORF1) protein from long interspersed nuclear element 1 (LINE-1) J Biol Chem 2003 278 8112 8117 10.1074/jbc.M210487200 12506113 · DOI
- Martin SL Bushman FD Nucleic acid chaperone activity of the ORF1 protein from the mouse LINE-1 retrotransposon Mol Cell Biol 2001 21 467 475 10.1128/MCB.21.2.467-475.2001 11134335 PMC86601 · DOI
- Feng Q Moran JV Kazazian HH Jr Boeke JD Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition Cell 1996 87 905 916 10.1016/S0092-8674(00)81997-2 8945517 · DOI · Paper page
- Mathias SL Scott AF Kazazian HH Jr Boeke JD Gabriel A Reverse transcriptase encoded by a human transposable element Science 1991 254 1808 10 10.1126/science.1722352 1722352 · DOI
- Han JS Boeke JD A highly active synthetic mammalian retrotransposon Nature 2004 429 314 318 10.1038/nature02535 15152256 · DOI
- An W Han JS Wheelan SJ Davis ES Coombes CE Ye P Triplett C Boeke JD Active retrotransposition by a synthetic L1 element in mice Proc Natl Acad Sci USA 2006 103 18662 18667 10.1073/pnas.0605300103 17124176 PMC1693719 · DOI
- Naas TP DeBerardinis RJ Moran JV Ostertag EM Kingsmore SF Seldin MF Hayashizaki Y Martin SL Kazazian HH An actively retrotransposing, novel subfamily of mouse L1 elements EMBO J 1998 17 590 597 10.1093/emboj/17.2.590 9430649 PMC1170408 · DOI
- Lindtner S Felber BK Kjems J An element in the 3' untranslated region of human LINE-1 retrotransposon mRNA binds NXF1(TAP) and can function as a nuclear export element RNA 2002 8 345 356 10.1017/S1355838202027759 12003494 PMC1370256 · DOI
- Alisch RS Garcia-Perez JL Muotri AR Gage FH Moran JV Unconventional translation of mammalian LINE-1 retrotransposons Genes Dev 2006 20 210 224 10.1101/gad.1380406 16418485 PMC1356112 · DOI
- Kulpa DA Moran JV Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles Nat Struct Mol Biol 2006 13 655 660 10.1038/nsmb1107 16783376 · DOI
- Belancio VP Whelton M Deininger P Requirements for polyadenylation at the 3' end of LINE-1 elements Gene 2007 390 98 107 10.1016/j.gene.2006.07.029 17023124 · DOI
- Belancio VP Hedges DJ Deininger P LINE-1 RNA splicing and influences on mammalian gene expression Nucleic Acids Res 2006 34 1512 1521 10.1093/nar/gkl027 16554555 PMC1415225 · DOI
- Kulpa DA Moran JV Ribonucleoprotein particle formation is necessary but not sufficient for LINE-1 retrotransposition Hum Mol Genet 2005 14 3237 3248 10.1093/hmg/ddi354 16183655 · DOI
- Haoudi A Semmes OJ Mason JM Cannon RE Retrotransposition-Competent Human LINE-1 Induces Apoptosis in Cancer Cells With Intact p53 J Biomed Biotechnol 2004 2004 185 194 10.1155/S1110724304403131 15467158 PMC555774 · DOI
- Wallace NA Belancio VP Deininger PL L1 mobile element expression causes multiple types of toxicity Gene 2008 419 75 81 10.1016/j.gene.2008.04.013 18555620 PMC3760205 · DOI
- Hatfield GW Roth DA Optimizing scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and Translation Engineering Biotechnol Annu Rev 2007 13 27 42 full_text 17875472
- Stemmer WP Crameri A Ha KD Brennan TM Heyneker HL Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides Gene 1995 164 49 53 10.1016/0378-1119(95)00511-4 7590320 · DOI
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Ardeljan, D., Steranka, J. P., Liu, C., Li, Z., Taylor, M. S., Payer, L. M., Gorbounov, M., Sarnecki, J. S., Deshpande, V., Hruban, R. H., et al. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0372-1 · Cited by 135 · see citing works
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Zhao, K., Du, J., Peng, Y., Li, P., Wang, S., Wang, Y., Hou, J., Kang, J., Zheng, W., Hua, S., et al. (2018) · Journal of Autoimmunity · doi:10.1016/j.jaut.2018.02.007 · Cited by 106 · see citing works
Fukuda, S., Varshney, A., Fowler, B. J., Wang, S.-B., Narendran, S., Ambati, K., Yasuma, T., Magagnoli, J., Leung, H., Hirahara, S., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2022751118 · Cited by 65 · see citing works
- Authors
- An, W., Dai, L., Niewiadomska, A. M., Yetil, A., O'Donnell, K. A., Han, J. S., & Boeke, J. D.
- Affiliations
- Johns Hopkins University (US)
- Corresponding author
- Boeke, Jef D
- Venue
- Mobile DNA
- Published
- 2011-02-14
- Volume
- 2
- Issue
- 1
- Pages
- 2-2
- ISSN
- 1759-8753 (ISSN-L)
- PMC
- PMC3045867
- OpenAlex
- W2116394990
- Cited by
- 67
- References
- 5
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 2 · 2023: 2 · 2022: 5 · 2021: 2 · 2020: 4 · 2019: 8 · 2018: 5 · 2017: 6 · 2016: 7 · 2015: 3 · 2014: 6 · 2013: 5 · 2012: 2
- FWCI
- 5.79
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Mobile DNA (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Institutes of Health
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
- Keywords
- LINE-1 retrotransposons, transcription elongation, L1 open reading frame, ORF1 protein
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