دورية أكاديمية
The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome.
العنوان: | The role of LTR retrotransposons in plant genetic engineering: how to control their transposition in the genome. |
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المؤلفون: | Ramakrishnan M; Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China., Papolu PK; State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China., Mullasseri S; Department of Zoology, St. Albert's College (Autonomous), Kochi, 682018, Kerala, India., Zhou M; State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China., Sharma A; State Key Laboratory of Subtropical Silviculture, Institute of Bamboo Research, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.; Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA., Ahmad Z; Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China., Satheesh V; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China., Kalendar R; Helsinki Institute of Life Science HiLIFE, University of Helsinki, Biocenter 3, Viikinkaari 1, F1-00014, Helsinki, Finland. ruslan.kalendar@helsinki.fi.; Institute of Plant Biology and Biotechnology (IPBB), Timiryazev Street 45, 050040, Almaty, Kazakhstan. ruslan.kalendar@helsinki.fi., Wei Q; Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China. weiqiang@njfu.edu.cn. |
المصدر: | Plant cell reports [Plant Cell Rep] 2023 Jan; Vol. 42 (1), pp. 3-15. Date of Electronic Publication: 2022 Nov 19. |
نوع المنشور: | Journal Article; Review |
اللغة: | English |
بيانات الدورية: | Publisher: Springer Country of Publication: Germany NLM ID: 9880970 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-203X (Electronic) Linking ISSN: 07217714 NLM ISO Abbreviation: Plant Cell Rep Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: Berlin ; New York : Springer, 1981- |
مواضيع طبية MeSH: | Retroelements*/genetics , Terminal Repeat Sequences*/genetics, Animals ; Genome, Plant/genetics ; Genes, Plant ; Plants/genetics |
مستخلص: | Key Message: We briefly discuss that the similarity of LTR retrotransposons to retroviruses is a great opportunity for the development of a genetic engineering tool that exploits intragenic elements in the plant genome for plant genetic improvement. Long terminal repeat (LTR) retrotransposons are very similar to retroviruses but do not have the property of being infectious. While spreading between its host cells, a retrovirus inserts a DNA copy of its genome into the cells. The ability of retroviruses to cause infection with genome integration allows genes to be delivered to cells and tissues. Retrovirus vectors are, however, only specific to animals and insects, and, thus, are not relevant to plant genetic engineering. However, the similarity of LTR retrotransposons to retroviruses is an opportunity to explore the former as a tool for genetic engineering. Although recent long-read sequencing technologies have advanced the knowledge about transposable elements (TEs), the integration of TEs is still unable either to control them or to direct them to specific genomic locations. The use of existing intragenic elements to achieve the desired genome composition is better than using artificial constructs like vectors, but it is not yet clear how to control the process. Moreover, most LTR retrotransposons are inactive and unable to produce complete proteins. They are also highly mutable. In addition, it is impossible to find a full active copy of a LTR retrotransposon out of thousands of its own copies. Theoretically, if these elements were directly controlled and turned on or off using certain epigenetic mechanisms (inducing by stress or infection), LTR retrotransposons could be a great opportunity to develop a genetic engineering tool using intragenic elements in the plant genome. In this review, the recent developments in uncovering the nature of LTR retrotransposons and the possibility of using these intragenic elements as a tool for plant genetic engineering are briefly discussed. (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.) |
References: | Alzohairy AM, Sabir JSM, Gyulai G, Younis RAA, Jansen RK, Bahieldin A (2014) Environmental stress activation of plant long-terminal repeat retrotransposons. Funct Plant Biol 41:557–567. (PMID: 10.1071/FP13339) Barbeau B, Mesnard J-M (2011) Making sense out of antisense transcription in human T-cell lymphotropic viruses (HTLVs). Viruses 3:456–468. (PMID: 10.3390/v3050456) Baum C, Schambach A, Bohne J, Galla M (2006) Retrovirus vectors: toward the Plentivirus? Mol Ther 13:1050–1063. (PMID: 10.1016/j.ymthe.2006.03.007) Belyayev A, Kalendar R, Brodsky L, Nevo E, Schulman AH, Raskina O (2010) Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat. Mob DNA 1:6. (PMID: 10.1186/1759-8753-1-6) Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C (2018) Ten things you should know about transposable elements. Genome Biol 19:199. (PMID: 10.1186/s13059-018-1577-z) Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, Reforgiato-Recupero G, Martin C (2012) Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24:1242–1255. (PMID: 10.1105/tpc.111.095232) Buttler CA, Chuong EB (2022) Emerging roles for endogenous retroviruses in immune epigenetic regulation. Immunol Rev 305:165–178. (PMID: 10.1111/imr.13042) Casacuberta JM, Grandbastien M-A (1993) Characterisation of LTR sequences involved in the protoplast specific expression of the tobacco Tnt1 retrotransposon. Nucleic Acids Res 21:2087–2093. (PMID: 10.1093/nar/21.9.2087) Cavrak VV, Lettner N, Jamge S, Kosarewicz A, Bayer LM, Mittelsten Scheid O (2014) How a retrotransposon exploits the plant’s heat stress response for its activation. PLoS Genet 10:e1004115. (PMID: 10.1371/journal.pgen.1004115) Chang Y-H, Keegan RM, Prazak L, Dubnau J (2019) Cellular labeling of endogenous retrovirus replication (CLEVR) reveals de novo insertions of the Gypsy retrotransposable element in cell culture and in both neurons and glial cells of aging fruit flies. PLoS Biol 17:e3000278. (PMID: 10.1371/journal.pbio.3000278) Cheng C, Daigen M, Hirochika H (2006) Epigenetic regulation of the rice retrotransposon Tos17. Mol Genet Genom 276:378–390. (PMID: 10.1007/s00438-006-0141-9) Cheng X, Zhang D, Cheng Z, Keller B, Ling HQ (2009) A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event. Genetics 181:1183–1193. (PMID: 10.1534/genetics.108.099150) Cho J, Paszkowski J (2017) Regulation of rice root development by a retrotransposon acting as a microRNA sponge. Elife 6:e30038. (PMID: 10.7554/eLife.30038) Courtial B, Feuerbach F, Eberhard S, Rohmer L, Chiapello H, Camilleri C, Lucas H (2001) Tnt1 transposition events are induced by in vitro transformation of Arabidopsis thaliana, and transposed copies integrate into genes. Mol Genet Genomics 265:32–42. (PMID: 10.1007/s004380000387) D’erfurth I, Cosson V, Eschstruth A, Lucas H, Kondorosi A, Ratet P (2003) Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J 34:95–106. (PMID: 10.1046/j.1365-313X.2003.01701.x) Diao X, Freeling M, Lisch D (2005) Horizontal transfer of a plant transposon. PLoS Biol 4:e5. (PMID: 10.1371/journal.pbio.0040005) Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y et al (2002) Sequence and analysis of rice chromosome 4. Nature 420:316–320. (PMID: 10.1038/nature01183) Finnegan EJ, Lawrence GJ, Dennis ES, Ellis JG (1993) Behaviour of modified Ac elements in flax callus and regenerated plants. Plant Mol Biol 22:625–633. (PMID: 10.1007/BF00047403) Fischer SEJ, Ruvkun G (2020) Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons. Proc Natl Acad Sci USA 117:5987–5996. (PMID: 10.1073/pnas.1919028117) Fukai E, Umehara Y, Sato S, Endo M, Kouchi H, Hayashi M, Stougaard J, Hirochika H (2010) Derepression of the plant chromovirus LORE1 induces germline transposition in regenerated plants. PLoS Genet 6:e1000868. (PMID: 10.1371/journal.pgen.1000868) Galindo-Gonzalez L, Mhiri C, Deyholos MK, Grandbastien MA (2017) LTR-retrotransposons in plants: Engines of evolution. Gene 626:14–25. (PMID: 10.1016/j.gene.2017.04.051) Grandbastien M-A, Spielmann A, Caboche M (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337:376–380. (PMID: 10.1038/337376a0) Grandi N, Tramontano E (2018) HERV envelope proteins: Physiological role and pathogenic potential in cancer and autoimmunity. Front Microbiol 9:462. (PMID: 10.3389/fmicb.2018.00462) Havecker ER, Gao X, Voytas DF (2004) The diversity of LTR retrotransposons. Genome Biol 5:225. (PMID: 10.1186/gb-2004-5-6-225) Hermant C, Torres-Padilla M-E (2021) TFs for TEs: the transcription factor repertoire of mammalian transposable elements. Genes Dev 35:22–39. (PMID: 10.1101/gad.344473.120) Hernández-Pinzón I, Cifuentes M, Hénaff E, Santiago N, Espinás ML, Casacuberta JM (2012) The Tnt1 retrotransposon escapes silencing in tobacco, its natural host. PLoS ONE 7:e33816. (PMID: 10.1371/journal.pone.0033816) Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture. EMBO J 12:2521–2528. (PMID: 10.1002/j.1460-2075.1993.tb05907.x) Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci USA 93:7783–7788. (PMID: 10.1073/pnas.93.15.7783) Hirochika H, Okamoto H, Kakutani T (2000) Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12:357–368. (PMID: 10.1105/tpc.12.3.357) Hosid E, Brodsky L, Kalendar R, Raskina O, Belyayev A (2012) Diversity of long terminal repeat retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops speltoides. Genetics 190:263–274. (PMID: 10.1534/genetics.111.134643) Huang J, Wang Y, Liu W, Xu S, Fan Q, Jian S, Tang T (2017) EARE-1, a transcriptionally active Ty1/Copia-like retrotransposon has colonized the genome of Excoecaria agallocha through horizontal transfer. Front Plant Sci 8:45. Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, Mccouch SR, Wessler SR (2002) Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161:1293–1305. (PMID: 10.1093/genetics/161.3.1293) Kakutani T, Jeddeloh JA, Flowers SK, Munakata K, Richards EJ (1996) Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci USA 93:12406–12411. (PMID: 10.1073/pnas.93.22.12406) Kalendar R, Tanskanen J, Immonen S, Nevo E, Schulman Alan H (2000) Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence. Proc Natl Acad Sci USA 97:6603–6607. (PMID: 10.1073/pnas.110587497) Kumar A, Hirochika H (2001) Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci 6:127–134. (PMID: 10.1016/S1360-1385(00)01860-4) Leblanc P, Desset S, Giorgi F, Taddei AR, Fausto AM, Mazzini M, Dastugue B, Vaury C (2000) Life cycle of an endogenous retrovirus, ZAM, in Drosophila melanogaster. J Virol 74:10658–10669. (PMID: 10.1128/JVI.74.22.10658-10669.2000) Lee S-I, Park K-C, Son J-H, Hwang Y-J, Lim K-B, Song Y-S, Kim J-H, Kim N-S (2013) Isolation and characterization of novel Ty1-copia-like retrotransposons from lily. Genome 56:495–503. (PMID: 10.1139/gen-2013-0088) Lee Y-S, Maple R, Dürr J, Dawson A, Tamim S, Del Genio C, Papareddy R, Luo A, Lamb JC, Amantia S (2021) A transposon surveillance mechanism that safeguards plant male fertility during stress. Nat Plants 7:34–41. (PMID: 10.1038/s41477-020-00818-5) Leigh F, Kalendar R, Lea V, Lee D, Donini P, Schulman AH (2003) Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques. Mol Genet Genom 269:464–474. (PMID: 10.1007/s00438-003-0850-2) Lerat E, Fablet M, Modolo L, Lopez-Maestre H, Vieira C (2017) TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes. Nucleic Acids Res 45:e17. Li C, Tang J, Hu Z, Wang J, Cao M (2020) A novel maize dwarf mutant generated by Ty1-copia LTR-retrotransposon insertion in Brachytic2 after spaceflight. Plant Cell Rep 39:1–16. (PMID: 10.1007/s00299-019-02498-8) Li F, Lee M, Esnault C, Wendover K, Guo Y, Atkins P, Zaratiegui M, Levin HL (2022) Identification of an integrase-independent pathway of retrotransposition. Sci Adv 8:eabm9390. (PMID: 10.1126/sciadv.abm9390) Lisch D (2013) How important are transposons for plant evolution? Nat Rev Genet 14:49–61. (PMID: 10.1038/nrg3374) Liu J-X, Liu J, Yang T-Y, Liu L-M, Qiu L-H, Gao Y-J, Duan W-X, Lei J-C, Liu H-J, Zhang R-H, He W-Z, Li S, Li Y-R, Wei R-C, Xiong F-Q (2022) Isolation and analysis of reverse transcriptase of Ty1-copia-like retrotransposons in sugarcane. Sugar Tech. https://doi.org/10.1007/s12355-021-01063-6. (PMID: 10.1007/s12355-021-01063-6) Luo Y, Tian D, Teo JCY, Ong KH, Yin Z (2020) Inactivation of retrotransposon Tos17 Chr 7 in rice cultivar Nipponbare through CRISPR/Cas9-mediated gene editing. Plant Biotechnol 37:69–75. (PMID: 10.5511/plantbiotechnology.20.0123a) Madsen LH, Fukai E, Radutoiu S, Yost CK, Sandal N, Schauser L, Stougaard J (2005) LORE1, an active low-copy-number Ty3-Gypsy retrotransposon family in the model legume Lotus japonicus. Plant J 44:372–381. (PMID: 10.1111/j.1365-313X.2005.02534.x) Marí-Ordóñez A, Marchais A, Etcheverry M, Martin A, Colot V, Voinnet O (2013) Reconstructing de novo silencing of an active plant retrotransposon. Nat Genet 45:1029–1039. (PMID: 10.1038/ng.2703) Masuta Y, Nozawa K, Takagi H, Yaegashi H, Tanaka K, Ito T, Saito H, Kobayashi H, Matsunaga W, Masuda S (2017) Inducible transposition of a heat-activated retrotransposon in tissue culture. Plant Cell Physiol 58:375–384. Melayah D, Bonnivard E, Chalhoub B, Audeon C, Grandbastien MA (2001) The mobility of the tobacco Tnt1 retrotransposon correlates with its transcriptional activation by fungal factors. Plant J 28:159–168. (PMID: 10.1046/j.1365-313X.2001.01141.x) Mhiri C, Morel J-B, Vernhettes S, Casacuberta JM, Lucas H, Grandbastien M-A (1997) The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress. Plant Mol Biol 33:257–266. (PMID: 10.1023/A:1005727132202) Mirouze M, Reinders J, Bucher E, Nishimura T, Schneeberger K, Ossowski S, Cao J, Weigel D, Paszkowski J, Mathieu O (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461:427–430. (PMID: 10.1038/nature08328) Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15:1771–1780. (PMID: 10.1105/tpc.012559) Ong-Abdullah M, Ordway JM, Jiang N, Ooi SE, Kok SY, Sarpan N, Azimi N, Hashim AT, Ishak Z, Rosli SK, Malike FA, Bakar NA, Marjuni M, Abdullah N, Yaakub Z, Amiruddin MD, Nookiah R, Singh R, Low ET, Chan KL, Azizi N, Smith SW, Bacher B, Budiman MA, Van Brunt A, Wischmeyer C, Beil M, Hogan M, Lakey N, Lim CC, Arulandoo X, Wong CK, Choo CN, Wong WC, Kwan YY, Alwee SS, Sambanthamurthi R, Martienssen RA (2015) Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525:533–537. (PMID: 10.1038/nature15365) Orozco-Arias S, Isaza G, Guyot R (2019) Retrotransposons in plant genomes: structure, identification, and classification through bioinformatics and machine learning. Int J Mol Sci 20:3837. (PMID: 10.3390/ijms20153837) Orozco-Arias S, Candamil-Cortés MS, Jaimes PA, Piña JS, Tabares-Soto R, Guyot R, Isaza G (2021) K-mer-based machine learning method to classify LTR-retrotransposons in plant genomes. PeerJ 9:e11456–e11456. (PMID: 10.7717/peerj.11456) Pelisson A, Mejlumian L, Robert V, Terzian C, Bucheton A (2002) Drosophila germline invasion by the endogenous retrovirus Gypsy: involvement of the viral env gene. Insect Biochem Mol Biol 32:1249–1256. (PMID: 10.1016/S0965-1748(02)00088-7) Peng Y, Zhang Y, Gui Y, An D, Liu J, Xu X, Li Q, Wang J, Wang W, Shi C (2019) Elimination of a retrotransposon for quenching genome instability in modern rice. Mol Plant 12:1395–1407. (PMID: 10.1016/j.molp.2019.06.004) Picault N, Chaparro C, Piegu B, Stenger W, Formey D, Llauro C, Descombin J, Sabot F, Lasserre E, Meynard D (2009) Identification of an active LTR retrotransposon in rice. Plant J 58:754–765. (PMID: 10.1111/j.1365-313X.2009.03813.x) Piontkivska H, Wales-Mcgrath B, Miyamoto M, Wayne ML (2021) ADAR editing in viruses: An evolutionary force to reckon with. Genome Biol Evol 13:evab240. (PMID: 10.1093/gbe/evab240) Pouteau S, Huttner E, Grandbastien MA, Caboche M (1991) Specific expression of the tobacco Tnt1 retrotransposon in protoplasts. EMBO J 10:1911–1918. (PMID: 10.1002/j.1460-2075.1991.tb07717.x) Quesneville H (2020) Twenty years of transposable element analysis in the Arabidopsis thaliana genome. Mob DNA 11:28. (PMID: 10.1186/s13100-020-00223-x) Rajput MK, Upadhyaya KC (2009) CARE1, a Ty3-Gypsy like LTR-retrotransposon in the food legume chickpea (Cicer arietinum L.). Genetica 136:429–437. (PMID: 10.1007/s10709-008-9343-x) Ramakrishnan M, Satish L, Kalendar R, Narayanan M, Kandasamy S, Sharma A, Emamverdian A, Wei Q, Zhou M (2021) The dynamism of transposon methylation for plant development and stress adaptation. Int J Mol Sci 22:11387. (PMID: 10.3390/ijms222111387) Ramakrishnan M, Satish L, Sharma A, Kurungara Vinod K, Emamverdian A, Zhou M, Wei Q (2022) Transposable elements in plants: recent advancements, tools and prospects. Plant Mol Biol Rep. https://doi.org/10.1007/s11105-022-01342-w. (PMID: 10.1007/s11105-022-01342-w) Roulin A, Piegu B, Wing RA, Panaud O (2008) Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza. Plant J 53:950–959. (PMID: 10.1111/j.1365-313X.2007.03388.x) Saika H, Mori A, Endo M, Toki S (2019) Targeted deletion of rice retrotransposon Tos17 via CRISPR/Cas9. Plant Cell Rep 38:455–458. (PMID: 10.1007/s00299-018-2357-7) Sato M, Kawabe T, Hosokawa M, Tatsuzawa F, Doi M (2011) Tissue culture-induced flower-color changes in Saintpaulia caused by excision of the transposon inserted in the flavonoid 3′, 5′ hydroxylase (F3′ 5′ H) promoter. Plant Cell Rep 30:929–939. (PMID: 10.1007/s00299-011-1016-z) Shastry KA, Sanjay HA (2020) Machine learning for bioinformatics. In: Srinivasa K, Siddesh G, Manisekhar S (eds) Statistical modelling and machine learning principles for bioinformatics techniques, tools, and applications Algorithms for intelligent systems. Springer Singapore, pp 25–39. Shelke RG, Das AB (2015) Analysis of genetic diversity in 21 genotypes of Indian banana using RAPDs and IRAPs markers. Proc Natl Acad Sci India Sect B Biol Sci 85:1027–1038. (PMID: 10.1007/s40011-015-0505-1) Sinzelle L, Izsvák Z, Ivics Z (2009) Molecular domestication of transposable elements: From detrimental parasites to useful host genes. Cell Mol Life Sci 66:1073–1093. (PMID: 10.1007/s00018-009-8376-3) Steinbauerová V, Neumann P, Macas J (2008) Experimental evidence for splicing of intron-containing transcripts of plant LTR retrotransposon Ogre. Mol Genet Genom 280:427–436. (PMID: 10.1007/s00438-008-0376-8) Sultana T, Zamborlini A, Cristofari G, Lesage P (2017) Integration site selection by retroviruses and transposable elements in eukaryotes. Nat Rev Genet 18:292–308. (PMID: 10.1038/nrg.2017.7) Suoniemi A, Narvanto A, Schulman AH (1996) The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol Biol 31:295–306. (PMID: 10.1007/BF00021791) Takeda S, Sugimoto K, Otsuki H, Hirochika H (1998) Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate. Plant Mol Biol 36:365–376. (PMID: 10.1023/A:1005911413528) Takeda S, Sugimoto K, Otsuki H, Hirochika H (1999) A 13-bp cis-regulatory element in the LTR promoter of the tobacco retrotransposon Tto1 is involved in responsiveness to tissue culture, wounding, methyl jasmonate and fungal elicitors. Plant J 18:383–393. (PMID: 10.1046/j.1365-313X.1999.00460.x) Tapia G, Verdugo I, Yañez M, Ahumada I, Theoduloz C, Cordero C, Poblete F, González E, Ruiz-Lara S (2005) Involvement of ethylene in stress-induced expression of the TLC1. 1 retrotransposon from Lycopersicon chilense Dun. Plant Physiol 138:2075–2086. (PMID: 10.1104/pp.105.059766) Thieme M, Lanciano S, Balzergue S, Daccord N, Mirouze M, Bucher E (2017) Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding. Genome Biol 18:134–134. (PMID: 10.1186/s13059-017-1265-4) Tsukahara S, Kawabe A, Kobayashi A, Ito T, Aizu T, Shin-I T, Toyoda A, Fujiyama A, Tarutani Y, Kakutani T (2012) Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata. Genes Dev 26:705–713. (PMID: 10.1101/gad.183871.111) Vicient CM, Casacuberta JM (2020) Additional ORFs in plant LTR-retrotransposons. Front Plant Sci 11:555. (PMID: 10.3389/fpls.2020.00555) Vicient CM, Kalendar R, Anamthawat-Jónsson K, Suoniemi A, Schulman AH (2000) Structure, functionality, and evolution of the BARE-1 retrotransposon of barley. In: McDonald JF (ed) Transposable elements and genome evolution. Georgia genetics review 1, vol 1. Springer Netherlands, pp 53–63. Vicient CM, JääSkeläInen MJ, Kalendar R, Schulman AH (2001) Active retrotransposons are a common feature of grass genomes. Plant Physiol 125:1283–1292. (PMID: 10.1104/pp.125.3.1283) Yilmaz S, Marakli S, Gozukirmizi N (2014) BAGY2 retrotransposon analyses in barley calli cultures and regenerated plantlets. Biochem Genet 52:233–244. (PMID: 10.1007/s10528-014-9643-z) Zervudacki J, Yu A, Amesefe D, Wang J, Drouaud J, Navarro L, Deleris A (2018) Transcriptional control and exploitation of an immune-responsive family of plant retrotransposons. EMBO J 37:e98482. (PMID: 10.15252/embj.201798482) Zhang H, Lang Z, Zhu JK (2018) Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol 19:489–506. (PMID: 10.1038/s41580-018-0016-z) Zhao Y, Xu T, Shen C-Y, Xu G-H, Chen S-X, Song L-Z, Li M-J, Wang L-L, Zhu Y, Lv W-T (2014) Identification of a retroelement from the resurrection plant Boea hygrometrica that confers osmotic and alkaline tolerance in Arabidopsis thaliana. PLoS ONE 9:e98098. (PMID: 10.1371/journal.pone.0098098) Zou J, Huss M, Abid A, Mohammadi P, Torkamani A, Telenti A (2018) A primer on deep learning in genomics. Nat Genet 51:12–18. (PMID: 10.1038/s41588-018-0295-5) |
معلومات مُعتمدة: | OR11465424 Ministry of Education and Science of the Republic of Kazakhstan; 163100028 Metasequoia Faculty Research Start-up Funding; S2019DQKJ2030 from the Jiangxi "Shuangqian" Programme; JC2019004 Natural Science Foundation for Distinguished Young Scholars of Nanjing Forestry University; 202211 the Project for Groundbreaking Achievements of Nanjing Forestry University |
فهرسة مساهمة: | Keywords: Genetic engineering; Plants; Retrotransposons; Retroviruses; Targeted integration; Transposable elements |
المشرفين على المادة: | 0 (Retroelements) |
تواريخ الأحداث: | Date Created: 20221119 Date Completed: 20230124 Latest Revision: 20230201 |
رمز التحديث: | 20231215 |
DOI: | 10.1007/s00299-022-02945-z |
PMID: | 36401648 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1432-203X |
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DOI: | 10.1007/s00299-022-02945-z |