594
Views
0
CrossRef citations to date
0
Altmetric
Review Articles

Transposable elements: a jump toward the future of expression vectors

ORCID Icon & ORCID Icon
Pages 792-808 | Received 03 Jul 2020, Accepted 12 Dec 2020, Published online: 23 Feb 2021

References

  • Kirk O, Borchert TV, Fuglsang CC. Industrial enzyme applications. Curr Opin Biotechnol. 2002;13(4):345–351.
  • Derouazi M, Toussaint B, Quénée L, et al. High-yield production of secreted active proteins by the Pseudomonas aeruginosa type III secretion system. Appl Environ Microbiol. 2008;74(11):3601–3604.
  • Hunter P. The prospects for recombinant proteins from transgenic animals: a few successes along with the advent of new technologies increase the allure of transgenic animals for the production of therapeutic human proteins. EMBO Rep. 2019;20(8):e48757.
  • Tavano OL, Berenguer-Murcia A, Secundo F, et al. Biotechnological applications of proteases in food technology. Compr Rev Food Sci Food Saf. 2018;17(2):412–436.
  • Maurer KH. Detergent proteases. Curr Opin Biotechnol. 2004;15(4):330–334.
  • Hunt JP, Yang SO, Wilding KM, et al. The growing impact of lyophilized cell-free protein expression systems. Bioengineered. 2017;8(4):325–330.
  • Oliver MJ. Why we need GMO crops in agriculture. Mo Med. 2014;111(6):492–507.
  • Zhang C, Wohlhueter R, Zhang H. Genetically modified foods: a critical review of their promise and problems. Food Sci Hum Wellness. 2016;5(3):116–123.
  • Kamle M, Kumar P, Patra JK, et al. Current perspectives on genetically modified crops and detection methods. 3 Biotech. 2017;7(3):219–219.
  • Schmeer M, Schleef M. Pharmaceutical grade large-scale plasmid DNA manufacturing process. Methods Mol Biol. 2014;1143:219–240.
  • Bakker NAM, de Boer R, Marie C, et al. Small-scale GMP production of plasmid DNA using a simplified and fully disposable production method. J Biotechnol: X. 2019;2:100007.
  • Quaak SGL, van den Berg JH, Toebes M, et al. GMP production of pDERMATT for vaccination against melanoma in a phase I clinical trial. Eur J Pharm Biopharm. 2008;70(2):429–438.
  • Sanber KS, Knight SB, Stephen SL, et al. Construction of stable packaging cell lines for clinical lentiviral vector production. Sci Rep. 2015;5:9021–9021.
  • Browning DF, Busby SJ. Local and global regulation of transcription initiation in bacteria. Nat Rev Microbiol. 2016;14(10):638–650.
  • Rosenberg LE, Rosenberg DD. Human genes and genomes. Waltham (MA): Academic Press; 2012. p. 97–116.
  • Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol. 2018;19(10):621–637.
  • Ottoz DSM, Rudolf F. Constitutive and regulated promoters in yeast: how to design and make use of promoters in S. cerevisiae. In: Smolke C, Lee SY, Nielsen J, Stephanopoulos G, editors. Synthetic biology: parts, devices and applications. Hoboken (NJ): Wiley; 2018. p. 107–130.
  • Panyukov VV, Ozoline ON. Promoters of Escherichia coli versus promoter islands: function and structure comparison. PLoS One. 2013;8(5):e62601.
  • Andersson R, Sandelin A. Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet. 2020;21(2):71–87.
  • Kallunki T, Barisic M, Jaattela M, et al. How to choose the right inducible gene expression system for mammalian studies? Cells. 2019;8(8):796.
  • Doshi A, Sadeghi F, Varadarajan N, et al. Small-molecule inducible transcriptional control in mammalian cells. Crit Rev Biotechnol. 2020;40(8):1131–1150.
  • Brand AH, Perrimon N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development. 1993;118(2):401–415.
  • Potter CJ, Tasic B, Russler EV, et al. The Q system: a repressible binary system for transgene expression, lineage tracing, and mosaic analysis. Cell. 2010;141(3):536–548.
  • McGuire SE, Roman G, Davis RL. Gene expression systems in Drosophila: a synthesis of time and space. Trends Genet. 2004;20(8):384–391.
  • Vaquerizas JM, Kummerfeld SK, Teichmann SA, et al. A census of human transcription factors: function, expression and evolution. Nat Rev Genet. 2009;10(4):252–263.
  • Brown AJ, James DC. Constructing strong cell type-specific promoters through informed design. Methods in Molecular Biology (Clifton, NJ). 2017;1651:131–145.
  • Lodish H, Berk AE, Kaiser CA, Krieger M, et al. Molecular cell biology, 8th ed. New York: W. H. Freeman; 2016
  • Lettice LA, Heaney SJH, Purdie LA. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet. 2003;12(14):1725–1735.
  • Robson MI, Ringel AR, Mundlos S. Regulatory landscaping: how enhancer-promoter communication is sculpted in 3D. Mol Cell. 2019;74(6):1110–1122.
  • Lewis EB. The theory and application of a new method of detecting chromosomal rearrangements in Drosophila melanogaster. The American Naturalist. 1954;88(841):225–239.
  • Geyer PK, Green MM, Corces VG. Tissue-specific transcriptional enhancers may act in trans on the gene located in the homologous chromosome: the molecular basis of transvection in Drosophila. Embo J. 1990;9(7):2247–2256.
  • Foecking MK, Hofstetter H. Powerful and versatile enhancer-promoter unit for mammalian expression vectors. Gene. 1986;45(1):101–105.
  • Hoppler S, Brown JD, Moon RT. Expression of a dominant-negative Wnt blocks induction of MyoD in Xenopus embryos. Genes Dev. 1996;10(21):2805–2817.
  • Hieber V, Dai X, Fau-Foreman M, et al. Induction of alpha1-tubulin gene expression during development and regeneration of the fish central nervous system. J Neurobiol. 1998;37(3):429–440.
  • Brand AH, Breeden L, Abraham J, et al. Characterization of a “silencer” in yeast: a DNA sequence with properties opposite to those of a transcriptional enhancer. Cell. 1985;41(1):41–48.
  • Ogbourne S, Antalis TM. Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes. Biochem J. 1998;331(1):1–14.
  • Maston GA, Evans SK, Green MR. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet. 2006;7:29–59.
  • Das AT, Tenenbaum L, Berkhout B. Tet-on systems for doxycycline-inducible gene expression. Curr Gene Ther. 2016;16(3):156–167.
  • Northcott PA, Lee C, Zichner T, et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature. 2014;511(7510):428–434.
  • Flavahan WA, Drier Y, Liau BB, et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2016;529(7584):110–114.
  • Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell. 2009;137(7):1194–1211.
  • West AG, Gaszner M, Felsenfeld G. Insulators: many functions, many mechanisms. Genes Dev. 2002;16(3):271–288.
  • Rodnina MV, Korniy N, Klimova M, et al. Translational recoding: canonical translation mechanisms reinterpreted. Nucleic Acids Res. 2020;48(3):1056–1067.
  • Helinski DR. Plasmids as vectors for gene cloning. Basic Life Sci. 1977;9:19–49.
  • Roy AL, Singer DS. Core promoters in transcription: old problem, new insights. Trends Biochem Sci. 2015;40(3):165–171.
  • Anish R, Hossain MB, Jacobson RH, et al. Characterization of transcription from TATA-Less promoters: identification of a new core promoter element XCPE2 and analysis of factor requirements. PLoS One. 2009;4(4):e5103.
  • Gagniuc P, Ionescu-Tirgoviste C. Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics. 2012;13:512.
  • Qin JY, Zhang L, Clift KL, et al. Systematic comparison of constitutive promoters and the doxycycline-inducible promoter. PLoS One. 2010;5(5):e10611.
  • Odell JT, Nagy F, Chua NH. Identification of DNA sequences required for activity of the cauliflower mosaic virus 35S promoter. Nature. 1985;313(6005):810–812.
  • Fromm M, Taylor LP, Walbot V. Expression of genes transferred into monocot and dicot plant cells by electroporation. Proc Natl Acad Sci USA. 1985;82(17):5824–5828.
  • Seternes T, Tonheim TC, Myhr AI, et al. A plant 35S CaMV promoter induces long-term expression of luciferase in Atlantic salmon. Sci Rep. 2016;6:25096.
  • de Villiers J, Olson L, Tyndall C, et al. Transcriptional ‘enhancers’ from SV40 and polyoma virus show a cell type preference. Nucleic Acids Res. 1982;10(24):7965–7976.
  • Ruvinsky I, Ruvkun G. Functional tests of enhancer conservation between distantly related species. Development. 2003;130(21):5133–5142.
  • Lai Y-T, Deem KD, Borràs-Castells F, et al. Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum. Development. 2018;145(7):dev160663.
  • Lin Y, Meng F, Fang C, et al. Rapid validation of transcriptional enhancers using agrobacterium-mediated transient assay. Plant Methods. 2019;15:21.
  • Umarov RK, Solovyev VV. Recognition of prokaryotic and eukaryotic promoters using convolutional deep learning neural networks. PLoS One. 2017;12(2):e0171410.
  • Nguyen TA, Jones RD, Snavely AR, et al. High-throughput functional comparison of promoter and enhancer activities. Genome Res. 2016;26(8):1023–1033.
  • Thurman RE, Rynes E, Humbert R, et al. The accessible chromatin landscape of the human genome. Nature. 2012;489(7414):75–82.
  • Cusanovich DA, Hill AJ, Aghamirzaie D, et al. A single-cell atlas of in vivo mammalian chromatin accessibility. Cell. 2018;174(5):1309–1324.
  • Erwin JA, Marchetto MC, Gage FH. Mobile DNA elements in the generation of diversity and complexity in the brain. Nat Rev Neurosci. 2014;15(8):497–506.
  • Biemont C, Vieira C. Genetics: junk DNA as an evolutionary force. Nature. 2006;443(7111):521–524.
  • Chenais B, Caruso A, Hiard S, et al. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene. 2012;509(1):7–15.
  • Hedges RW, Jacob AE. Transposition of ampicillin resistance from RP4 to other replicons. Mol Gen Genet. 1974;132(1):31–40.
  • Shapiro JA. Mutations caused by the insertion of genetic material into the galactose operon of Escherichia coli. J Mol Biol. 1969;40(1):93–105.
  • Mc Clintock B. The origin and behavior of mutable loci in maize. Proc Natl Acad Sci USA. 1950;36:344–355.
  • Feschotte C, Pritham EJ. DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 2007;41:331–368.
  • Ivics Z, Izsvák Z. The expanding universe of transposon technologies for gene and cell engineering. Mob Dna. 2010;1(1):25.
  • Ivics Z, Izsvak Z. Transposons for gene therapy! Curr Gene Ther. 2006;6(5):593–607.
  • VandenDriessche T, Ivics Z, Izsvak Z, et al. Emerging potential of transposons for gene therapy and generation of induced pluripotent stem cells. Blood. 2009;114(8):1461–1468.
  • Hudecek M, Izsvák Z, Johnen S, et al. Going non-viral: the Sleeping Beauty transposon system breaks on through to the clinical side. Crit Rev Biochem Mol Biol. 2017;52(4):355–380.
  • Chandler M. Prokaryotic DNA transposons: classes and mechanism. In: eLS. Chichester: John Wiley & Sons, Ltd; 2017. doi: 10.1002/9780470015902.a0000590.pub2
  • Wicker T, Sabot F, Hua-Van A, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007;8(12):973–982.
  • Kapitonov VV, Jurka J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet. 2008;9(5):411–412.
  • Makałowski W, Gotea V, Pande A, et al. Evolutionary genomics: statistical and computational methods. New York (NY): Springer; 2019. p. 177–207.
  • Li Y, Dooner HK. Excision of Helitron transposons in maize. Genetics. 2009;182(1):399–402.
  • Eickbush TH, Eickbush DG. Transposable elements: evolution. In: eLS. Chichester: John Wiley & Sons, Ltd; 2006. doi:10.1038/npg.els.0005130
  • Bennetzen JL. Transposable element contributions to plant gene and genome evolution. Plant Mol Biol. 2000;42(1):251–269.
  • Carbone L, Harris RA, Gnerre S, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014;513(7517):195–201.
  • Meyer TJ, Held U, Nevonen KA, et al. The flow of the gibbon LAVA element is facilitated by the LINE-1 retrotransposition machinery. Genome Biol Evol. 2016;8(10):3209–3225.
  • Chuong EB, Elde NC, Feschotte C. Regulatory activities of transposable elements: from conflicts to benefits. Nat Rev Genet. 2017;18(2):71–86.
  • Kunarso G, Chia N-Y, Jeyakani J, et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat Genet. 2010;42(7):631–634.
  • Moschetti R, Palazzo A, Lorusso P, et al. “What you need, baby, i got it”: transposable elements as suppliers of Cis-operating sequences in Drosophila. Biology (Basel). 2020;9(2):25.
  • Sundaram V, Wysocka J. Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes. Philos Trans R Soc Lond B Biol Sci. 2020;375(1795):20190347.
  • Kellner M, Makałowski W. Transposable elements significantly contributed to the core promoters in the human genome. Sci China Life Sci. 2019;62(4):489–497.
  • Feschotte C. Transposable elements and the evolution of regulatory networks. Nat Rev Genet. 2008;9(5):397–405.
  • Miao B, Fu S, Lyu C, et al. Tissue-specific usage of transposable element-derived promoters in mouse development. Genome Biol. 2020;21(1):255.
  • Schön U, Diem O, Leitner L, et al. Human endogenous retroviral long terminal repeat sequences as cell type-specific promoters in retroviral vectors. J Virol. 2009;83(23):12643–12650.
  • Wang L, Chang S, Guan J, et al. Tissue-specific methylation of long interspersed nucleotide element-1 of Homo sapiens (L1Hs) during human embryogenesis and roles in neural tube defects. Curr Mol Med. 2015;15(5):497–507.
  • Emera D, Wagner GP. Transformation of a transposon into a derived prolactin promoter with function during human pregnancy. Proc Nat Acad Sci. 2012:109(28):11246–11251.
  • Smith CEL, Alexandraki A, Cordery SF, et al. A tissue-specific promoter derived from a SINE retrotransposon drives biallelic expression of PLAGL1 in human lymphocytes. PLoS One. 2017;12(9):e0185678.
  • Davis MP, Carrieri C, Saini HK, et al. Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution. EMBO Rep. 2017;18(7):1231–1247.
  • Chishima T, Iwakiri J, Hamada M. Identification of transposable elements contributing to tissue-specific expression of long non-coding RNAs. Genes. 2018;9(1):23.
  • Maksakova IA, Mager DL. Transcriptional regulation of early transposon elements, an active family of mouse long terminal repeat retrotransposons. J Virol. 2005;79(22):13865–13874.
  • Vandecraen J, Chandler M, Aertsen A, et al. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol. 2017;43(6):709–730.
  • Notwell JH, Chung T, Heavner W, et al. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex. Nat Commun. 2015;6:6644.
  • Conte C, Dastugue B, Vaury C. Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes. Mol Cell Biol. 2002;22(6):1767–1777.
  • Todd CD, Deniz O, Taylor D, et al. Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells. Elife. 2019;8:e44344.
  • Gause M, Morcillo P, Dorsett D. Insulation of enhancer-promoter communication by a gypsy transposon insert in the Drosophila cut gene: cooperation between suppressor of hairy-wing and modifier of mdg4 proteins. Mol Cell Biol. 2001;21(14):4807–4817.
  • Cai HN, Levine M. The gypsy insulator can function as a promoter-specific silencer in the Drosophila embryo. Embo J. 1997;16(7):1732–1741.
  • Bire S, Casteret S, Piégu B, et al. Mariner transposons contain a silencer: possible role of the polycomb repressive complex 2. PLoS Genet. 2016;12(3):e1005902.
  • Liu N, Lee CH, Swigut T, et al. Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Nature. 2018;553(7687):228–232.
  • Robbez-Masson L, Tie CHC, Conde L, et al. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes. Genome Res. 2018;28(6):836–845.
  • Wang J, Vicente-García C, Seruggia D, et al. MIR retrotransposon sequences provide insulators to the human genome. Proc Natl Acad Sci USA. 2015;112(32):E4428–E4437.
  • Lunyak VV, Prefontaine GG, Núñez E, et al. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science. 2007;317(5835):248–251.
  • Schmidt D, Schwalie PC, Wilson MD, et al. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell. 2012;148(1–2):335–348.
  • Chandler M, Fayet O. Translational frameshifting in the control of transposition in bacteria. Mol Microbiol. 1993;7(4):497–503.
  • Palazzo A, Marconi S, Specchia V, et al. Functional characterization of the Bari1 transposition system. PLoS One. 2013;8(11):e79385.
  • Palazzo A, Moschetti R, Caizzi R, et al. The Drosophila mojavensis Bari3 transposon: distribution and functional characterization. Mob Dna. 2014;5:21.
  • Palazzo A, Lovero D, D’Addabbo P, et al. Identification of Bari transposons in 23 sequenced Drosophila genomes reveals novel structural variants, mites and horizontal transfer. PLoS One. 2016;11(5):e0156014.
  • Yuan YW, Wessler SR. The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Proc Natl Acad Sci USA. 2011;108(19):7884–7889.
  • Tellier M, Bouuaert CC, Chalmers R. Mariner and the ITm superfamily of transposons. Microbiol Spectr. 2015;3(2):MDNA3.
  • Palazzo A, Caizzi R, Viggiano L, et al. Does the promoter constitute a barrier in the horizontal transposon transfer process? Insight from Bari transposons. Genome Biol Evol. 2017;9(6):1637–1645.
  • Palazzo A, Lorusso P, Miskey C, et al. Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes. Mob Dna. 2019;10:13.
  • Minervini CF, Ruggieri S, Traversa M, et al. Evidences for insulator activity of the 5'UTR of the Drosophila melanogaster LTR-retrotransposon ZAM. Mol Genet Genomics. 2010;283(5):503–509.
  • Mora C, Tittensor DP, Adl S, et al. How many species are there on Earth and in the ocean? PLoS Biol. 2011;9(8):e1001127.
  • Hartl DL, Lozovskaya ER, Nurminsky DI, et al. What restricts the activity of mariner-like transposable elements. Trends Genet. 1997;13(5):197–201.
  • Gilbert C, Feschotte C. Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Curr Opin Genet Dev. 2018;49:15–24.
  • Groth AC, Fish M, Nusse R, et al. Construction of transgenic Drosophila by using the site-specific integrase from phage phiC31. Genetics. 2004;166(4):1775–1782.
  • Iwaki T, Figuera M, Ploplis VA, et al. Rapid selection of Drosophila S2 cells with the puromycin resistance gene. Biotechniques. 2003;35(3):482–484.
  • Lum L, Yao S, Mozer B, et al. Identification of Hedgehog pathway components by RNAi in Drosophila cultured cells. Science. 2003;299(5615):2039–2045.
  • Kunzelmann S, Bottcher R, Schmidts I, et al. A comprehensive toolbox for genome editing in cultured drosophila melanogaster cells. G3 (Bethesda)). 2016;6(6):1777–1785.
  • Wang JW, Beck ES, McCabe BD. A modular toolset for recombination transgenesis and neurogenetic analysis of Drosophila. PLoS One. 2012;7(7):e42102.
  • Buchman A, Akbari OS. Site-specific transgenesis of the Drosophila melanogaster Y-chromosome using CRISPR/Cas9. Insect Mol Biol. 2019;28(1):65–73.
  • Pfeiffer BD, Ngo T-TB, Hibbard KL, et al. Refinement of tools for targeted gene expression in Drosophila. Genetics. 2010;186(2):735–755.
  • Fuchs NV, Kraft M, Tondera C, et al. Expression of the human endogenous retrovirus (HERV) group HML-2/HERV-K does not depend on canonical promoter elements but is regulated by transcription factors Sp1 and Sp3. J Virol. 2011;85(7):3436–3448.
  • Montesion M, Williams ZH, Subramanian RP, et al. Promoter expression of HERV-K (HML-2) provirus-derived sequences is related to LTR sequence variation and polymorphic transcription factor binding sites. Retrovirology. 2018;15(1):57.
  • Lin H, Wang Q, Shen Q, et al. Genetic engineering of microorganisms for biodiesel production. Bioengineered. 2013;4(5):292–304.
  • Sticklen MB. Plant genetic engineering for biofuel production: towards affordable cellulosic ethanol. Nat Rev Genet. 2008;9(6):433–443.
  • Tyagi S, Kumar R, Das A, et al. CRISPR-Cas9 system: a genome-editing tool with endless possibilities. J Biotechnol. 2020;319:36–53.
  • Marsano RM, Leronni D, D’Addabbo P, et al. Mosquitoes LTR retrotransposons: a deeper view into the genomic sequence of Culex quinquefasciatus. PLoS One. 2012;7(2):e30770.
  • Jain M, Koren S, Miga KH, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36(4):338–345.
  • Marsano RM, Giordano E, Messina G, et al. A new portrait of constitutive heterochromatin: lessons from Drosophila melanogaster. Trends Genet. 2019;35(9):615–631.
  • Yasuhara JC, DeCrease CH, Wakimoto BT. Evolution of heterochromatic genes of Drosophila. Proc Natl Acad Sci USA. 2005;102(31):10958–10963.
  • Caizzi R, Moschetti R, Piacentini L, et al. Comparative genomic analyses provide new insights into the evolutionary dynamics of heterochromatin in Drosophila. PLoS Genet. 2016;12(8):e1006212.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.