Abstract
To study the influence of genomic context on transgene expression, we have determined the T-DNA structure, flanking DNA sequences, and chromosomal location of four independent transgene loci in tobacco. Two of these loci were stably expressed in the homozygous condition over many generations, whereas the other two loci became unstable after several generations of homozygosity. The stably expressed loci comprised relatively simple T-DNA arrangements that were flanked on at least one side by plant DNA containing AT-rich regions that bind to nuclear matrices in vitro. Of the unstably expressed loci, one consisted of multiple incomplete T-DNA copies, and the second contained a single intact T-DNA; in both cases, however, binary vector sequences were directly contiguous to a right T-DNA border. Fluorescence in situ hybridization demonstrated that the two stably expressed inserts were present in the vicinity of telomeres. The two unstably expressed inserts occupied intercalary and paracentromeric locations, respectively. Results on the stability of transgene expression in F1 progeny obtained by intercrossing the four lines and the sensitivity of the four transgene loci to inactivation in the presence of an unlinked "trans-silencing" locus are also presented. The findings are discussed in the context of repetitive DNA sequences and the allotetraploid nature of the tobacco genome.
Full Text
The Full Text of this article is available as a PDF (3.1 MB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Allshire R. C., Javerzat J. P., Redhead N. J., Cranston G. Position effect variegation at fission yeast centromeres. Cell. 1994 Jan 14;76(1):157–169. doi: 10.1016/0092-8674(94)90180-5. [DOI] [PubMed] [Google Scholar]
- Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- Assaad F. F., Tucker K. L., Signer E. R. Epigenetic repeat-induced gene silencing (RIGS) in Arabidopsis. Plant Mol Biol. 1993 Sep;22(6):1067–1085. doi: 10.1007/BF00028978. [DOI] [PubMed] [Google Scholar]
- Avramova Z., SanMiguel P., Georgieva E., Bennetzen J. L. Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1. Plant Cell. 1995 Oct;7(10):1667–1680. doi: 10.1105/tpc.7.10.1667. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bennetzen J. L. The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol. 1996 Sep;4(9):347–353. doi: 10.1016/0966-842x(96)10042-1. [DOI] [PubMed] [Google Scholar]
- Bernardi G. The human genome: organization and evolutionary history. Annu Rev Genet. 1995;29:445–476. doi: 10.1146/annurev.ge.29.120195.002305. [DOI] [PubMed] [Google Scholar]
- Bustos M. M., Guiltinan M. J., Jordano J., Begum D., Kalkan F. A., Hall T. C. Regulation of beta-glucuronidase expression in transgenic tobacco plants by an A/T-rich, cis-acting sequence found upstream of a French bean beta-phaseolin gene. Plant Cell. 1989 Sep;1(9):839–853. doi: 10.1105/tpc.1.9.839. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cluster P. D., O'Dell M., Metzlaff M., Flavell R. B. Details of T-DNA structural organization from a transgenic Petunia population exhibiting co-suppression. Plant Mol Biol. 1996 Dec;32(6):1197–1203. doi: 10.1007/BF00041406. [DOI] [PubMed] [Google Scholar]
- Dobie K. W., Lee M., Fantes J. A., Graham E., Clark A. J., Springbett A., Lathe R., McClenaghan M. Variegated transgene expression in mouse mammary gland is determined by the transgene integration locus. Proc Natl Acad Sci U S A. 1996 Jun 25;93(13):6659–6664. doi: 10.1073/pnas.93.13.6659. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dobie K., Mehtali M., McClenaghan M., Lathe R. Variegated gene expression in mice. Trends Genet. 1997 Apr;13(4):127–130. doi: 10.1016/s0168-9525(97)01097-4. [DOI] [PubMed] [Google Scholar]
- Grandbastien M. A. Retroelements in higher plants. Trends Genet. 1992 Mar;8(3):103–108. doi: 10.1016/0168-9525(92)90198-d. [DOI] [PubMed] [Google Scholar]
- Hobbs S. L., Warkentin T. D., DeLong C. M. Transgene copy number can be positively or negatively associated with transgene expression. Plant Mol Biol. 1993 Jan;21(1):17–26. doi: 10.1007/BF00039614. [DOI] [PubMed] [Google Scholar]
- Jorgensen R. A., Cluster P. D., English J., Que Q., Napoli C. A. Chalcone synthase cosuppression phenotypes in petunia flowers: comparison of sense vs. antisense constructs and single-copy vs. complex T-DNA sequences. Plant Mol Biol. 1996 Aug;31(5):957–973. doi: 10.1007/BF00040715. [DOI] [PubMed] [Google Scholar]
- Kilby N. J., Leyser H. M., Furner I. J. Promoter methylation and progressive transgene inactivation in Arabidopsis. Plant Mol Biol. 1992 Oct;20(1):103–112. doi: 10.1007/BF00029153. [DOI] [PubMed] [Google Scholar]
- Kononov M. E., Bassuner B., Gelvin S. B. Integration of T-DNA binary vector 'backbone' sequences into the tobacco genome: evidence for multiple complex patterns of integration. Plant J. 1997 May;11(5):945–957. doi: 10.1046/j.1365-313x.1997.11050945.x. [DOI] [PubMed] [Google Scholar]
- Linn F., Heidmann I., Saedler H., Meyer P. Epigenetic changes in the expression of the maize A1 gene in Petunia hybrida: role of numbers of integrated gene copies and state of methylation. Mol Gen Genet. 1990 Jul;222(2-3):329–336. doi: 10.1007/BF00633837. [DOI] [PubMed] [Google Scholar]
- Martineau B., Voelker T. A., Sanders R. A. On Defining T-DNA. Plant Cell. 1994 Aug;6(8):1032–1033. doi: 10.1105/tpc.6.8.1032. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Matassi G., Melis R., Macaya G., Bernardi G. Compositional bimodality of the nuclear genome of tobacco. Nucleic Acids Res. 1991 Oct 25;19(20):5561–5567. doi: 10.1093/nar/19.20.5561. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Matsumoto S., Ito Y., Hosoi T., Takahashi Y., Machida Y. Integration of Agrobacterium T-DNA into a tobacco chromosome: possible involvement of DNA homology between T-DNA and plant DNA. Mol Gen Genet. 1990 Dec;224(3):309–316. doi: 10.1007/BF00262423. [DOI] [PubMed] [Google Scholar]
- Matzke A. J., Neuhuber F., Park Y. D., Ambros P. F., Matzke M. A. Homology-dependent gene silencing in transgenic plants: epistatic silencing loci contain multiple copies of methylated transgenes. Mol Gen Genet. 1994 Aug 2;244(3):219–229. doi: 10.1007/BF00285449. [DOI] [PubMed] [Google Scholar]
- Meyer P., Saedler H. HOMOLOGY-DEPENDENT GENE SILENCING IN PLANTS. Annu Rev Plant Physiol Plant Mol Biol. 1996 Jun;47(NaN):23–48. doi: 10.1146/annurev.arplant.47.1.23. [DOI] [PubMed] [Google Scholar]
- Mittelsten Scheid O., Jakovleva L., Afsar K., Maluszynska J., Paszkowski J. A change of ploidy can modify epigenetic silencing. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7114–7119. doi: 10.1073/pnas.93.14.7114. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mlynarova L., Keizer LCP., Stiekema W. J., Nap J. P. Approaching the Lower Limits of Transgene Variability. Plant Cell. 1996 Sep;8(9):1589–1599. doi: 10.1105/tpc.8.9.1589. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Moscone E. A., Matzke M. A., Matzke A. J. The use of combined FISH/GISH in conjunction with DAPI counterstaining to identify chromosomes containing transgene inserts in amphidiploid tobacco. Chromosoma. 1996 Dec;105(5):231–236. [PubMed] [Google Scholar]
- Neuhuber F., Park Y. D., Matzke A. J., Matzke M. A. Susceptibility of transgene loci to homology-dependent gene silencing. Mol Gen Genet. 1994 Aug 2;244(3):230–241. doi: 10.1007/BF00285450. [DOI] [PubMed] [Google Scholar]
- Ohba T., Yoshioka Y., Machida C., Machida Y. DNA rearrangement associated with the integration of T-DNA in tobacco: an example for multiple duplications of DNA around the integration target. Plant J. 1995 Jan;7(1):157–164. doi: 10.1046/j.1365-313x.1995.07010157.x. [DOI] [PubMed] [Google Scholar]
- Papp I., Iglesias V. A., Moscone E. A., Michalowski S., Spiker S., Park Y. D., Matzke M. A., Matzke A. J. Structural instability of a transgene locus in tobacco is associated with aneuploidy. Plant J. 1996 Sep;10(3):469–478. doi: 10.1046/j.1365-313x.1996.10030469.x. [DOI] [PubMed] [Google Scholar]
- Park Y. D., Papp I., Moscone E. A., Iglesias V. A., Vaucheret H., Matzke A. J., Matzke M. A. Gene silencing mediated by promoter homology occurs at the level of transcription and results in meiotically heritable alterations in methylation and gene activity. Plant J. 1996 Feb;9(2):183–194. doi: 10.1046/j.1365-313x.1996.09020183.x. [DOI] [PubMed] [Google Scholar]
- Pawlowski W. P., Somers D. A. Transgene inheritance in plants genetically engineered by microprojectile bombardment. Mol Biotechnol. 1996 Aug;6(1):17–30. doi: 10.1007/BF02762320. [DOI] [PubMed] [Google Scholar]
- Pröls F., Meyer P. The methylation patterns of chromosomal integration regions influence gene activity of transferred DNA in Petunia hybrida. Plant J. 1992 Jul;2(4):465–475. doi: 10.1046/j.1365-313x.1992.t01-20-00999.x. [DOI] [PubMed] [Google Scholar]
- Raff J. W., Kellum R., Alberts B. The Drosophila GAGA transcription factor is associated with specific regions of heterochromatin throughout the cell cycle. EMBO J. 1994 Dec 15;13(24):5977–5983. doi: 10.1002/j.1460-2075.1994.tb06943.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ramanathan V., Veluthambi K. Transfer of non-T-DNA portions of the Agrobacterium tumefaciens Ti plasmid pTiA6 from the left terminus of TL-DNA. Plant Mol Biol. 1995 Sep;28(6):1149–1154. doi: 10.1007/BF00032676. [DOI] [PubMed] [Google Scholar]
- Saccone S., De Sario A., Della Valle G., Bernardi G. The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes. Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):4913–4917. doi: 10.1073/pnas.89.11.4913. [DOI] [PMC free article] [PubMed] [Google Scholar]
- SanMiguel P., Tikhonov A., Jin Y. K., Motchoulskaia N., Zakharov D., Melake-Berhan A., Springer P. S., Edwards K. J., Lee M., Avramova Z. Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996 Nov 1;274(5288):765–768. doi: 10.1126/science.274.5288.765. [DOI] [PubMed] [Google Scholar]
- Sperisen C., Ryals J., Meins F. Comparison of cloned genes provides evidence for intergenomic exchange of DNA in the evolution of a tobacco glucan endo-1,3-beta-glucosidase gene family. Proc Natl Acad Sci U S A. 1991 Mar 1;88(5):1820–1824. doi: 10.1073/pnas.88.5.1820. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Spiker S., Thompson W. F. Nuclear Matrix Attachment Regions and Transgene Expression in Plants. Plant Physiol. 1996 Jan;110(1):15–21. doi: 10.1104/pp.110.1.15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Suter-Crazzolara C., Brzobohaty B., Gazdova B., Schell J., Reiss B. T-DNA integrations in a new family of repetitive elements of Nicotiana tabacum. J Mol Evol. 1995 Oct;41(4):498–504. doi: 10.1007/BF00160322. [DOI] [PubMed] [Google Scholar]
- Ten Hoopen R., Robbins T. P., Fransz P. F., Montijn B. M., Oud O., Gerats AGM., Nanninga N. Localization of T-DNA Insertions in Petunia by Fluorescence in Situ Hybridization: Physical Evidence for Suppression of Recombination. Plant Cell. 1996 May;8(5):823–830. doi: 10.1105/tpc.8.5.823. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tinland B., Hohn B. Recombination between prokaryotic and eukaryotic DNA: integration of Agrobacterium tumefaciens T-DNA into the plant genome. Genet Eng (N Y) 1995;17:209–229. [PubMed] [Google Scholar]
- van der Graaff E., den Dulk-Ras A., Hooykaas P. J. Deviating T-DNA transfer from Agrobacterium tumefaciens to plants. Plant Mol Biol. 1996 Jun;31(3):677–681. doi: 10.1007/BF00042239. [DOI] [PubMed] [Google Scholar]