Chromatin structure of integrated T-DNA in crown gall tumors

Effect of chromatin upon Agrobacterium T-DNA integration and transgene expression

Agrobacterium tumefaciens transfers DNA (T-DNA) to plant cells, where it integrates into the plant genome. Little is known about how T-DNA chooses sites within the plant chromosome for integration. Previous studies indicated that T-DNA preferentially integrates into transcriptionally active regions of the genome, especially in 5'-promoter regions. This would make sense, considering that chromatin structure surrounding active promoters may be more "open" and accessible to foreign DNA. However, recent results suggest that this seemingly non-random pattern of integration may be an artifact of selection bias, and that T-DNA may integrate more randomly than previously thought. In this chapter, I discuss the history of these observations and the role chromatin proteins may play in T-DNA integration and transgene expression. Understanding how chromatin conformation may influence T-DNA integration will be important in developing strategies for reproducible and stable transgene expression, and for gene targeting.

A chromosomal paracentric inversion associated with T-DNA integration in Arabidopsis

T-DNA integration in the nuclear plant genome may lead to rearrangements of the plant target site. Here we present evidence for a chromosomal inversion of 26 cM bordered by two T-DNAs in direct orientation, which is linked to the mgoun2 mutation. The integration sites of the T-DNAs map at positions 80 and 106 of chromosome I and we show that each T-DNA is bordered by plant sequences from positions 80 and 106, respectively. Although the T-DNAs are physically distant, they are genetically closely linked. In addition, three markers located on the chromosome segment between the two T-DNA integration sites show no recombination with the mgo2 mutation. We show that the inversion cannot be a consequence of a recombination event between the two T-DNAs, but that the integration of the T-DNAs and the inversion were two temporally linked events. T-DNA integration mechanisms that could have led to this inversion are discussed.

Transgene organization in rice engineered through direct DNA transfer supports a two-phase integration mechanism mediated by the establishment of integration hot spots

Organization of transgenes in rice transformed through direct DNA transfer strongly suggests a two-phase integration mechanism. In the "preintegration" phase, transforming plasmid molecules (either intact or partial) are spliced together. This gives rise to rearranged transgenic sequences, which upon integration do not contain any interspersed plant genomic sequences. Subsequently, integration of transgenic DNA into the host genome is initiated. Our experiments suggest that the original site of integration acts as a hot spot, facilitating subsequent integration of successive transgenic molecules at the same locus. The resulting transgenic locus may have plant DNA separating the transgenic sequences. Our data indicate that transformation through direct DNA transfer, specifically particle bombardment, generally results in a single transgenic locus as a result of this two-phase integration mechanism. Transgenic plants generated through such processes may, therefore, be more amenable to breeding programs as the single transgenic locus will be easier to characterize genetically. Results from direct DNA transfer experiments suggest that in the absence of protein factors involved in exogenous DNA transfer through Agrobacterium, the qualitative and/or quantitative efficiency of transformation events is not compromised. Our results cast doubt on the role of Agrobacterium vir genes in the integration process.

Effect of T-DNA configuration on transgene expression

T-DNA vectors were constructed which carry a beta-glucuronidase (gusA) gene fused to the promoter of the nopaline synthase (nos) gene and the 3' end of the octopine synthase (ocs) gene. This reporter gene was cloned at different locations and orientations towards the right T-DNA border. For each construct, between 30 and 60 stably transformed calli were analysed for beta-glucuronidase activity. Depending on the T-DNA configuration, distinct populations of gusA-expressing calli were obtained. Placing the reporter gene in the middle of the T-DNA results in relatively low expression levels and a limited inter-transformant variability. Placing the gene with its promoter next to the right border led to an increase in both the mean activity and the variability level. With this construct, some of the calli expressed the gusA gene at levels four to five times higher than the mean. In all these series, at least 30% of the calli contained reporter gene activities that were less than half of the mean expression level. Separating the gusA gene from the right T-DNA border by an additional 3'-untranslated region, derived from the nos gene, resulted in an increase in the mean expression to a level almost four times higher than that of constructions carrying the reporter gene in the middle of the T-DNA. Moreover, the number of transformants with extremely low activities decreased by at least 50% and this resulted in significantly lower inter-transformant variability independently of the orientation of the reporter gene on the T-DNA.

Transgene expression variability (position effect) of CAT and GUS reporter genes driven by linked divergent T-DNA promoters

Forty-five individually transformed clonal tobacco callus lines were simultaneously assayed for both chloramphenicol acetyltransferase (CAT) and beta-glucuronidase (GUS) activity resulting from expression of introduced reporter genes driven by the adjacent and divergent mannopine (mas) promoters. Excluding lines in which one or both of the enzyme activities was essentially zero, the activities of the reporter genes varied by as much as a factor of 136 (CAT) and 175 (GUS) between individual transformants. Superimposed upon the high degree of inter-clonal expression variability was an intra-clonal variability of 3-4-fold. The observed degree of intra-clonal reporter gene activity may be more extreme because of the regulatory characteristics of the mannopine promoters, but must still be addressed when considering the limitations of reporter gene-based analysis of transgene function and structure. There was no consistent correlation between the expression levels of the introduced CAT and GUS genes since the ratio of GUS to CAT activities (nmol min-1 mg-1) within individual lines varied from 0.05 to 49. Even divergent transcription from two directly adjacent promoter regions (both contained within a 479 bp TR-DNA fragment) is insufficient to guarantee concurrent expression of two linked transgenes. Our quantitative data were compared to published data of transgene expression variability to examine the overall distribution of expression levels in individual transformants. The resulting frequency distribution indicates that most transformants express introduced transgenes at relatively low levels, suggesting that a potentially large number of Agrobacterium-mediated transformation events may result in silent transgenes.

DNA structures associated with autonomously replicating sequences from plants

DNA fragments capable of conferring autonomous replicating ability to plasmids inSaccharomyces cerevisiae were isolated from four different plant genomes and from the Ti plasmid ofAgrobacterium tumefaciens. The DNA structure of these autonomously replicating sequences (ARSs) as well as two from yeast were studied using retardation during polyacrylamide gel electrophoresis and computer analysis as measures of sequence-dependent DNA structures. Bent DNA was found to be associated with the ARS elements. An 11 bp ARS consensus sequence required for ARS function was also identified in the elements examined and was flanked by unusually straight structures which were rich in A+T content. These results show that the ARS elements from genomes of higher plants have structural and sequence features in common with ARS elements from yeast and higher animals.

Constitutive and light-induced DNAseI hypersensitive sites in the rbcS genes of pea (Pisum sativum)

The chromatin structure of pea (Pisum sativum) rbcS genes in inactive (root), potentially active (dark-grown leaf), and active states (light-grown leaf) was analysed using (a) pancreatic DNAseI to detect general DNAseI sensitivity and DNAseI-hypersensitive sites, and (b) methyl-sensitive restriction endonucleases to probe for cytosine methylation within the promoter region. We showed that within the same organ individual members of the pea rbcS multigene family are differentially sensitive to DNAseI suggesting differential protection in nuclei. During light activation general DNAseI sensitivity increases in some genes, especially their 5' upstream regulatory sequences. DNAseI-hypersensitive sites are constitutively present in 5' upstream regulatory sequences around positions -335, -465, -650, and -945 (5' constitutive domain) and in the coding region around position +340, +450, +530, +640, and +810 (3' constitutive domain). One additional hypersensitive site appears after light induction (inducible site). This region is centred around position -190 and flanked by light-responsive elements (LREs). In spite of changes in the chromatin structure of rbcS genes during their transition from an inactive to an active state, their cytosine methylation at Alu I, Fnu 4HI, Hae III, Sau 3AI and Sau 96I sites in the promoter region remains uniform.

Deoxyribonuclease I sensitivity of the T-DNA ipt gene is associated with gene expression

We have analyzed the chromatin structure of the T-DNA isopentenyl transferase gene, ipt, in four Nicotiana tabacum crown gall tumor lines. These four transformed lines contain identical T-DNA inserts and are derivatives of a single clone that did not exhibit any tumorous properties and contained a highly methylated, nonexpressed copy of T-DNA. One of the derivatives also does not exhibit tumorous properties, and the T-DNA of this line is not expressed. The other three lines have reverted to tumorous growth either spontaneously or after treatment with the inhibitor of DNA methylation, 5-azacytidine. Concomitant with this reversion to tumorous growth, expression of the ipt gene of these lines has reinitiated. In the lines that express the ipt gene, the chromatin structure of this gene exists in a conformation that is more accessible to DNase I than in the line in which this gene is not expressed. The level of ipt expression and DNase I sensitivity was independent of the process by which the transformed cell lines reverted to tumorous growth. The relationship of chromatin structure to gene expression and DNA methylation in these lines is discussed.

Establishment of the nuclear location of Dictyostelium discoideum plasmids

The nuclear location of the Dictyostelium discoideum plasmids was studied using a biochemical approach based on the presence of plasmid sequences in nucleosomes. This analysis revealed that all four of the known plasmids (Ddp1, Ddp2, Ddp3, Ddp5) are present in chromatin. This evidence establishes that the D. discoideum plasmids are not cytoplasmic but located in the nucleus. D. discoideum is unique among eukaryotes in possessing a group of nonhomologous endogenous plasmids in its nucleus. These plasmids are excellent starting material for construction of nuclear transformation and expression vectors. Such vectors upon transformation into D. discoideum are also present in chromatin as expected for DNA located in the nucleus.