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Enhancer–promoter interference and its prevention in transgenic plants

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Abstract

Biotechnology has several advantages over conventional breeding for the precise engineering of gene function and provides a powerful tool for the genetic improvement of agronomically important traits in crops. In particular, it has been exploited for the improvement of multiple traits through the simultaneous introduction or stacking of several genes driven by distinct tissue-specific promoters. Since transcriptional enhancer elements have been shown to override the specificity of nearby promoters in a position- and orientation-independent manner, the co-existence of multiple enhancers/promoters within a single transgenic construct could be problematic as it has the potential to cause the mis-expression of transgene product(s). In order to develop strategies with, which to prevent such interference, a clear understanding of the mechanisms underlying enhancer-mediated activation of target promoters, as well as the identification of DNA sequences that function to block these interactions in plants, will be necessary. To date, little is known concerning enhancer function in plants and only a very limited number of enhancer-blocking insulators that operate in plant species have been identified. In this review, we discuss the current knowledge surrounding enhancer–promoter interactions, as well as possible means of minimizing such interference during plant transformation experiments.

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Abbreviations

35S :

35S cauliflower mosaic virus promoter/enhancer

AGIP :

Arabidopsis AGAMOUS second intron-derived promoter

GUS :

β-Glucuronidase

MAR:

Matrix attachment region

TBS :

Transformation booster sequence

References

  • Bae E, Calhoun VC, Levine M, Lewis EB, Drewell RA (2002) Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex. Proc Natl Acad Sci USA 99:16847–16852

    Article  PubMed  CAS  Google Scholar 

  • Barges S, Mihaly J, Galloni M, Hagstrom K, Muller M, Shanower G, Schedl P, Gyurkovics H, Karch F (2000) The Fab-8 boundary defines the distal limit of the bithorax complex iab-7 domain and insulates iab-7 from initiation elements and a PRE in the adjacent iab-8 domain. Development 127:779–790

    PubMed  CAS  Google Scholar 

  • Bell AC, West AG, Felsenfeld G (1999) The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98:387–396

    Article  PubMed  CAS  Google Scholar 

  • Bi X, Broach JR (2006) UASrpg can function as a heterochromatin boundary element in yeast. Genes Dev 13:1089–1101

    Article  Google Scholar 

  • Blackwood EM, Kadonaga JT (1998) Going the distance: a current view of enhancer action. Science 281:60–63

    Article  PubMed  CAS  Google Scholar 

  • Bondarenko VA, Liu YV, Jiang YI, Studitsky VM (2003) Communication over a large distance: enhancers and insulators. Biochem Cell Biol 81:241–251

    Article  PubMed  CAS  Google Scholar 

  • Brinch-Pedersen H, Hatzack F, Sorensen LD, Holm PB (2003) Concerted action of endogenous and heterologous phytase on phytic acid degradation in seed of transgenic wheat (Triticum aestivum L.). Transgen Res 12:649–659

    Article  CAS  Google Scholar 

  • Broders F, Scherrer K (1987) Transcription of the alpha globin gene domain in normal and AEV-transformed chicken erythroblasts: mapping of giant globin-specific RNA including embryonic and adult genes. Mol Gen Genet 209:210–220

    Article  PubMed  CAS  Google Scholar 

  • Bulger M, Groudine M (1999) Looping versus linking: toward a model for long-distance gene activation. Genes Dev 13:2465–2477

    Article  PubMed  CAS  Google Scholar 

  • Busch MA, Bomblies K, Weigel D (1999) Activation of a floral homeotic gene in Arabidopsis. Science 285:585–587

    Article  PubMed  CAS  Google Scholar 

  • Butler JE, Kadonaga JT (2001) Enhancer–promoter specificity mediated by DPE or TATA core promoter motifs. Gene Dev 15:2515–2519

    Article  PubMed  CAS  Google Scholar 

  • Clark RM, Wagler TN, Quijada P, Doebley J (2006) A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescence architecture. Nature Genet 38:594–597

    Article  PubMed  CAS  Google Scholar 

  • Chopra VS, Cande J, Hong JW, Levine M (2009) Stalled Hox promoters as chromosomal boundaries. Genes Dev 23:1505–1509

    Article  PubMed  CAS  Google Scholar 

  • Chung JH, Whiteley M, Felsenfeld G (1993) A 5′ element of the chicken β-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell 74:505–514

    Article  PubMed  CAS  Google Scholar 

  • Datta K, Vasquez A, Tu J, Torrizo L, Alam MF, Oliva N, Abrigo E, Khush GS, Datta SK (1998) Constitutive and tissue-specific differential expression of the cryIA (b) gene in transgenic rice plants conferring resistance to rice insect pest. Theor Appl Genet 97:20–30

    Article  CAS  Google Scholar 

  • Dobi KC, Winston F (2007) Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Mol Cell Biol 27:5575–5586

    Article  PubMed  CAS  Google Scholar 

  • Donoghue M, Ernst H, Wentworth B, Nadal-Ginard B, Rosenthal N (1988) A muscle-specific enhancer is located at the 3′ end of the myosin light-chain 1/3 gene locus. Genes Dev 2:1779–1790

    Article  PubMed  CAS  Google Scholar 

  • Dorsett D (1999) Distant liaisons: long-range enhancer–promoter interactions in Drosophila. Curr Opin Genet Dev 9:505–514

    Article  PubMed  CAS  Google Scholar 

  • Drewell RA, Bae E, Burr J, Lewis EB (2002) Transcription defines the embryonic domains of cis-regulatory activity at the Drosophila bithorax complex. Proc Natl Acad Sci USA 99:16853–16858

    Article  PubMed  CAS  Google Scholar 

  • Engelbrecht CC, Schoof H, Böhm S (2004) Conservation, diversification and expression of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 5:1–17

    Article  Google Scholar 

  • Fiering S, Whitelaw E, Martin DIK (2000) To be or not to be active: the stochastic nature of enhancer action. Bioessays 22:381–387

    Article  PubMed  CAS  Google Scholar 

  • Filippova GN, Fagerlie S, Klenova EM, Myers C, Dehner Y, Goodwin G, Neiman PE, Collins SJ, Lobanenkov VV (1996) An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol Cell Biol 16:2802–2813

    PubMed  CAS  Google Scholar 

  • Foster E, Hattori J, Labbé H, Ouellet T, Fobert PR, James LE, Iyer VN, Miki BL (1999) A tobacco cryptic constitutive promoter, tCUP, revealed by T-DNA tagging. Plant Mol Biol 41:45–55

    Article  PubMed  CAS  Google Scholar 

  • Fox PC, Vasil V, Vasil IK, Gurley WB (1992) Multiple ocs-like elements required for efficient transcription of the mannopine synthase gene of T-DNA in maize protoplasts. Plant Mol Biol 20:219–233

    Article  PubMed  CAS  Google Scholar 

  • Gan S, Xie M (2002) Genetic insulator for preventing influence by another gene promoter. USA patent # 20060174370

  • Gaszner M, Felsenfeld G (2006) Insulators: Exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet 7:703–713

    Article  PubMed  CAS  Google Scholar 

  • Gaszner M, Vazquez J, Schedl P (1999) The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer–promoter interaction. Genes Dev 13:2098–2107

    Article  PubMed  CAS  Google Scholar 

  • Geyer PK (1997) The role of insulator elements in defining domains of gene expression. Curr Opin Genet Dev 7:242–248

    Article  PubMed  CAS  Google Scholar 

  • Geyer PK, Spana C, Corces VG (1986) On the molecular mechanism of gypsy-induced mutations at the yellow locus of Drosophila melanogaster. EMBO J 5:2657–2662

    PubMed  CAS  Google Scholar 

  • Golovnin A, Melnikova L, Volkov I, Kostuchenko M, Galkin AV, Georgiev P (2008) ‘Insulator bodies’ are aggregates of proteins but not of insulators. EMBO Rep 9:440–445

    Article  PubMed  CAS  Google Scholar 

  • Gudynaite-Savitch L, Johnson DA, Miki BLA (2009) Strategies to mitigate transgene–promoter interactions. Plant Biotechnol J 7:472–485

    Article  PubMed  CAS  Google Scholar 

  • Hajdukiewicz P, Svab Z, Maliga P (1994) The small, versatile pPZP family of Agrobacterium binary vectors for plant transformation. Plant Mol Biol 25:989–994

    Article  PubMed  CAS  Google Scholar 

  • Hily JM, Singer SD, Yang Y, Liu Z (2009) A transformation booster sequence (TBS) from Petunia hybrida functions as an enhancer-blocking insulator in Arabidopsis thaliana. Plant Cell Rep 28:1095–1104

    Article  PubMed  CAS  Google Scholar 

  • Hinz U, Wolk A, Renkawitz-Pohl R (1992) Ultrabithorax is a regulator of β3 tubulin expression in the Drosophila visceral mesoderm. Development 116:543–554

    PubMed  CAS  Google Scholar 

  • Ho Y, Elefant F, Liebhaber SA, Cooke NE (2006) Locus control region transcription plays an active role in long-range gene activation. Mol Cell 23:365–375

    Article  PubMed  CAS  Google Scholar 

  • Jack J, Dorsett D, DeLotto Y, Liu S (1991) Expression of the cut locus in the Drosophila wing margin is required for cell type specification and is regulated by a distant enhancer. Development 113:735–747

    PubMed  CAS  Google Scholar 

  • Jagannath A, Bandyopadhyay P, Arumugam N, Gupta V, Kumar P, Pental D (2001) The use of a Spacer DNA fragment insulates the tissue-specific expression of a cytotoxic gene (barnase) and allow high-frequency generation of transgenic male sterile lines in Brassica juncea L. Mol Breeding 8:11–23

    Article  CAS  Google Scholar 

  • Juven-Gershon T, Hsu JY, Kadonaga JT (2008) Caudal, a key developmental regulator, is a DPE-specific transcriptional factor. Genes Dev 22:2823–2830

    Article  PubMed  CAS  Google Scholar 

  • Kadauke S, Blobel GA (2009) Chromatin loops in gene regulation. Biochim Biophys Acta 1789:17–25

    PubMed  CAS  Google Scholar 

  • Kay R, Chan A, Daly M, McPherson J (1987) Duplication of CaMV 35S promoter sequences creates a strong enhancer for plant genes. Science 236:1299–1302

    Article  PubMed  CAS  Google Scholar 

  • Kellum R, Schedl P (1992) A group of scs elements function as domain boundaries in an enhancer-blocking assay. Mol Cell Biol 12:2424–2431

    PubMed  CAS  Google Scholar 

  • Kim SR, Kim Y, An G (1993) Identification of methyl jasmonate and salicylic acid response elements from the nopaline synthase (nos) promoter. Plant Physiol 103:97–103

    Article  PubMed  CAS  Google Scholar 

  • Kim T, Abdullaev Z, Smith A, Ching K, Loukinov D, Green R, Zhang M, Lobanenkov V, Ren B (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128:1231–1245

    Article  PubMed  CAS  Google Scholar 

  • Kononowicz H, Wang YE, Habeck LL, Gelvin SB (1992) Subdomains of the octopine synthase upstream activating element direct cell-specific expression in transgenic tobacco plants. Plant Cell 4:17–27

    Article  PubMed  CAS  Google Scholar 

  • Ling J, Ainol L, Zhang L, Yu X, Pi W, Tuan D (2004) HS2 enhancer function is blocked by a transcriptional terminator inserted between the enhancer and the promoter. J Biol Chem 279:51704–51713

    Article  PubMed  CAS  Google Scholar 

  • Ling J, Baibakov B, Pi W, Emerson BM, Tuan D (2005) The HS2 enhancer of the β-globin locus control region initiates synthesis of non-coding, polyadenylated RNAs independent of a cis-linked globin promoter. J Mol Biol 350:883–896

    Article  PubMed  CAS  Google Scholar 

  • Liu Z, Zhou C, Wu K (2008) Creation and analysis of a novel chimeric promoter for the complete containment of pollen- and seed-mediated gene flow. Plant Cell Rep 27:995–1004

    Article  PubMed  CAS  Google Scholar 

  • Moon H, Filippova G, Loukinov D, Pugacheva E, Chen Q, Smith ST, Munhall A, Grewe B, Bartkuhn M, Arnold R, Burke LJ, Renkawitz-Pohl R, Ohlsson R, Zhou J, Renkawitz R, Lobanenkov V (2005) CTCF is conserved from Drosophila to humans and confers enhancer blocking of the Fab-8 insulator. EMBO Rep 6:165–170

    Article  PubMed  CAS  Google Scholar 

  • Morris JR, Chen J-I, Geyer PK, Wu C-t (1998) Two modes of transvection: Enhancer action in trans and bypass of a chromatin insulator in cis. Proc Natl Acad Sci 95:10740–10745

    Article  PubMed  CAS  Google Scholar 

  • Müller H-P, Matthias P, Schaffner W (1990) A transcriptional terminator between enhancer and promoter does not affect remote transcriptional control. Somat Cell Mol Genet 16:351–360

    Article  PubMed  Google Scholar 

  • Nagaya SN, Yoshida K, Kato K, Akasaka K (2001) An insulator element from the sea urchin Hemicentrotus pulcherrimus suppresses variation in transgene expression in cultured tobacco cells. Mol Genet Genom 265:405–413

    Article  CAS  Google Scholar 

  • Namciu SJ, Blochlinger KB, Fournier REK (1998) Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogaster. Mol Cell Biol 18:2382–2391

    PubMed  CAS  Google Scholar 

  • Ni M, Cui D, Einstein J, Narasimhulu S, Vergara CE, Gelvin SB (1995) Strength and tissue specificity of chimeric promoters derived from the octopine and mannopine synthase genes. Plant J 7:661–676

    Article  CAS  Google Scholar 

  • Odell JT, Knowlton S, Lin W, Mauvais J (1988) Properties of an isolated transcription stimulating sequence derived from the cauliflower mosaic virus 35S promoter. Plant Mol Biol 10:263–272

    Article  CAS  Google Scholar 

  • Ouwerkerk PBF, de Kam RJ, Hoge JHC, Meijer AH (2001) Glucocorticoid-inducible gene expression in rice. Planta 213:370–378

    Article  PubMed  CAS  Google Scholar 

  • Park SH, Lee B-M, Salas MG, Srivatanakul M, Smith RH (2000) Shorter T-DNA or additional virulence genes improve Agrobacterium-mediated transformation. Theor Appl Genet 101:1015–1020

    Article  CAS  Google Scholar 

  • Parkhurst SM, Harrison DA, Remington MP, Spana C, Kelley RL, Coyne RS, Corces VG (1988) The Drosophila su(Hw) gene, which controls the phenotypic effect of the gypsy transposable element, encodes a putative DNA-binding protein. Genes Dev 2:1205–1215

    Article  PubMed  CAS  Google Scholar 

  • Ptashne M, Gann A (1997) Transcriptional activation by recruitment. Nature 386:569–577

    Article  PubMed  CAS  Google Scholar 

  • Raab JR, Kamakaka RT (2010) Insulators and promoters: closer than we think. Nat Rev Genet 11:439–446

    Article  PubMed  CAS  Google Scholar 

  • Razin S, Rynditch A, Borunova V, Ioudinkova E, Smalko V, Scherrer K (2004) The 33 kb transcript of the chicken α-globin gene domain is part of the nuclear matrix. J Cell Biochem 92:445–457

    Article  PubMed  CAS  Google Scholar 

  • Ren S, Johnston JS, Shippen DE, McKnight T (2004) TELEMERASE ACTIVATOR1 induces telomerase activity and potentiates responses to auxin in Arabidopsis. Plant Cell 16:2910–2922

    Article  PubMed  CAS  Google Scholar 

  • Rosenthal N, Berglund EB, Wentworth BM, Donoghue M, Winter B, Bober E, Braun T, Arnold H-H (1990) A highly conserved enhancer downstream of the human MLC1/3 locus is a target for multiple myogenic determination factors. Nucl Acids Res 18:6239–6246

    Article  PubMed  CAS  Google Scholar 

  • Sieburth LE, Meyerowitz E (1997) Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. Plant Cell 9:355–365

    Article  PubMed  CAS  Google Scholar 

  • Singer SD, Cox KD, Liu Z (2010a) Both the constitutive Cauliflower Mosaic Virus 35S and tissue-specific AGAMOUS enhancers activate transcription autonomously in Arabidopsis thaliana. Plant Mol Biol 74:293–305

    Article  PubMed  CAS  Google Scholar 

  • Singer SD, Hily J-M, Liu Z (2010b) A 1 kb bacteriophage lambda fragment functions as an insulator to effectively block enhancer–promoter interactions in Arabidopsis thaliana. Plant Mol Biol Rep 28:69–76

    Article  CAS  Google Scholar 

  • Steinwaerder DS, Lieber A (2000) Insulation from viral transcriptional regulatory elements improves inducible transgene expression from adenovirus vectors in vitro and in vivo. Gene Ther 7:556–567

    Article  PubMed  CAS  Google Scholar 

  • Tchurikov NA, Kretova OV, Moiseeva ED, Sosin DV (2009) Evidence for RNA synthesis in the intergenic region between enhancer and promoter and its inhibition by insulators in Drosophila melanogaster. Nucl Acids Res 37:111–122

    Article  PubMed  CAS  Google Scholar 

  • van der Geest AHM, Hall TC (1997) The β-phaseolin 5′ matrix attachment region acts as an enhancer facilitator. Plant Mol Biol 33:553–557

    Article  PubMed  Google Scholar 

  • Wallace JA, Felsenfeld G (2007) We gather together: insulators and genome organization. Curr Opin Genet Dev 17:400–407

    Article  PubMed  CAS  Google Scholar 

  • Walters MC, Fiering S, Eidemiller J, Magis W, Groudine M, Martin DIK (1995) Enhancers increase the probability but not the level of gene expression. Proc Natl Acad Sci USA 92:7125–7129

    Article  PubMed  CAS  Google Scholar 

  • Wang Q, Carroll J, Brown M (2005) Spatial and temporal recruitment of androgen receptor and its coactivators involves chromosomal looping and polymerase tracking. Mol Cell 19:631–642

    Article  PubMed  CAS  Google Scholar 

  • Weterings K, Schrauwen J, Wullems G, Twell D (1995) Functional dissection of the promoter of the pollen-specific gene NTP303 reveals a novel pollen-specific, and conserved cis-regulatory element. Plant J 8:55–63

    Article  PubMed  CAS  Google Scholar 

  • Yang Y, Singer SD, Liu Z (2010) Evaluation and comparison of the insulation efficiency of three enhancer-blocking insulators in plants. Plant Cell Tiss Org (in press)

  • Ye X, Liang M, Meng X, Ren X, Chen H, Li ZY, Ni S, Lieber A, Hu F (2003) Insulation from viral transcriptional regulatory elements enables improvement to hepatoma-specific gene expression from adenovirus vectors. Biochem Biophys Res Commun 307:759–764

    Article  PubMed  CAS  Google Scholar 

  • Yoo SY, Bomblies K, Yoo SK, Yang JW, Choi MS, Lee JS, Weigel D, Ahn JH (2005) The 35S promoter used in a selectable marker gene of a plant transformation vector affects the expression of the transgene. Planta 221:523–530

    Article  PubMed  CAS  Google Scholar 

  • Zheng X, Deng W, Luo K, Duan H, Chen Y, McAvoy R, Song S, Pei Y, Li Y (2007) The cauliflower mosaic virus (CaMV) 35S promoter sequence alters the level and patterns of activity of adjacent tissue- and organ-specific gene promoters. Plant Cell Rep 26:1195–1203

    Article  PubMed  CAS  Google Scholar 

  • Zhong X-P, Krangel MS (1997) An enhancer-blocking element between α and δ gene segments within the human T cell receptor α/δ locus. Proc Natl Acad Sci USA 94:5219–5224

    Article  PubMed  CAS  Google Scholar 

  • Zhou J, Ashe H, Burks C, Levine M (1999) Characterization of the transvection mediating region of the abdominal-B locus in Drosophila. Development 126:3057–3065

    PubMed  CAS  Google Scholar 

  • Zhu X, Ling J, Zhang L, Pi W, Wu M, Tuan D (2007) A facilitated tracking and transcription mechanism of long-range enhancer function. Nucl Acids Res 35:5532–5544

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

The authors wish to thank Mr. Dennis Bennett (USDA-ARS, Kearneysville, WV) for his indispensable assistance. This work was funded by the USDA-ARS Headquarter 2007 class of postdoctoral grants and USDA CSREES BRAG grants (2006-03701; 2009-01067).

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  1. Stacy D. Singer & Kerik D. Cox

    Present address: Department of Plant Pathology, New York State Agricultural Experiment Station, Cornell University, 630 West North Street, Geneva, NY, 14456, USA

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  1. USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA

    Stacy D. Singer & Zongrang Liu

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  1. Stacy D. Singer
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  2. Kerik D. Cox
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Correspondence to Zongrang Liu.

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Communicated by R. Reski.

A contribution to the Special Issue: Plant Biotechnology in Support of the Millennium Development Goals.

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Singer, S.D., Cox, K.D. & Liu, Z. Enhancer–promoter interference and its prevention in transgenic plants. Plant Cell Rep 30, 723–731 (2011). https://doi.org/10.1007/s00299-010-0977-7

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