Flank matrix attachment regions (MARs) from chicken, bean, yeast or tobacco do not prevent homology-dependent trans-silencing in transgenic tobacco plants

Effects of a petunia scaffold/matrix attachment region on copy number dependency and stability of transgene expression in Nicotiana tabacum

Transgenes in genetically modified plants are often not reliably expressed during development or in subsequent generations. Transcriptional gene silencing (TGS) as well as post-transcriptional gene silencing (PTGS) have been shown to occur in transgenic plants depending on integration pattern, copy number and integration site. In an effort to reduce position effects, to prevent read-through transcription and to provide a more accessible chromatin structure, a P35S-ß-glucuronidase (P35S-gus) transgene flanked by a scaffold/matrix attachment region from petunia (Petun-SAR), was introduced in Nicotiana tabacum plants by Agrobacterium tumefaciens mediated transformation. It was found that Petun-SAR mediates enhanced expression and copy number dependency up to 2 gene copies, but did not prevent gene silencing in transformants with multiple and rearranged gene copies. However, in contrast to the non-SAR transformants where silencing was irreversible and proceeded during long-term vegetative propagation and in progeny plants, gus expression in Petun-SAR plants was re-established in the course of development. Gene silencing was not necessarily accompanied by DNA methylation, while the gus transgene could still be expressed despite considerable CG methylation within the coding region.

The Role of Nuclear Matrix Attachment Regions in Plants

Regions of DNA that bind to the nuclear matrix, or nucleoskeleton, are known as Matrix Attachment Regions (MARs). MARs are thought to play an important role in higher-order structure and chromatin organization within the nucleus. MARs are also thought to act as boundaries of chromosomal domains that act to separate regions of gene-rich, decondensed euchromatin from highly repetitive, condensed heterochromatin. Herein I will present evidence that MARs do indeed act as domain boundaries and can prevent the spread of silencing into active genes. Many fundamental questions remain unanswered about how MARs function in the nucleus. New findings in epigenetics indicate that MARs may also play an important role in the organization of genes and the eventual transport of their mRNAs through the nuclear pore.

Soybean mosaic virus helper component-protease enhances somatic embryo production and stabilizes transgene expression in soybean

Soybean mosaic virus (SMV) helper component protease (HC-Pro), a suppressor of post-transcriptional gene silencing, was evaluated for its ability to enhance production of soybean hygromycin-resistant somatic embryos (HR-SEs), and stabilize transgene expression. Immature soybean cotyledonary explants were co-cultured with Agrobacterium tumefaciens strain KYRT1 harboring either pCAMBIA1302, carrying a hygromycin phosphotransferase gene (hpt) and a gene encoding green fluorescent protein; pCAMBIA1305.1, carrying hpt and beta-glucuronidase (uidA) genes; pG2-HC-Pro, a derivative of pCAMBIA1305.1 containing SMV G2 HC-Pro; or pG5-HC-Pro, a derivative of pCAMBIA1305.1 containing SMV G5 HC-Pro, but lacking uidA. Significantly (rho<0.02) higher numbers of HR-SEs were obtained from explants transformed with Agrobacterium harboring either pG2-HC-Pro or pG5-HC-Pro than with either of the vector controls (pCAMBIA1302 or pCAMBIA1305.1). Beta-glucuronidase (GUS) expression was significantly (rho<0.003) higher in 50-day-old transgenic plants expressing GUS along with SMV-HC-Pro and in SMV-infected GUS transgenic plants than in transgenic plants expressing GUS alone. Together, these data suggest that SMV-HC-Pro enhanced recovery of HR-SEs by suppressing silencing of the hygromycin phosphotransferase gene.

Matrix attachment regions increase the efficiency and stability of RNA-mediated resistance to tomato spotted wilt virus in transgenic tobacco

Matrix attachment regions (MARs) are DNA elements that can increase and stabilize transgene expression. We investigated the effect of the RB7 MAR on transgenic virus resistance. Constructs for resistance to tomato spotted wilt virus (TSWV) with and without flanking RB7 MARs were used to transform tobacco and produce homozygous lines. The population with the MAR construct had a significantly higher percentage of TSWV resistant plants in the R1 generation than the nonMAR population. Each resistant line was advanced to the R4 generation, and significantly fewer MAR lines lost resistance over generations compared to the nonMAR population. Lines with TSWV resistance in growth chamber tests were also resistant in field trials. Two lines that were resistant in the R1 generation and susceptible in the R4 were examined in more detail in order to determine if transcriptional silencing of the transgene was occurring in the later generation. Short interfering 21-25 nt RNAs from the transgene that are characteristic of post-transcriptional gene silencing (PTGS) were present in the resistant R1 plants, but not the susceptible R4 plants, indicating that virus resistance was associated with PTGS of the transgene. Loss of resistance was accompanied by an increase in promoter methylation in both lines. In line M41, the transgene was fully silenced at the transcriptional level in the R4 as shown by nuclear run-on assays. In line NM13, transgene transcription and RNA accumulation was still present in the R4 generation, but the level of transcription was not sufficient to trigger PTGS, suggesting that this line may have partial transcriptional silencing. These results are consistent with the concept that MARs may prevent transcriptional silencing.

Gene stacking in transgenic plants--the challenge for 21st century plant biotechnology

One of the major technical hurdles impeding the advance of plant genetic engineering and biotechnology is the fact that the expression or manipulation of multiple genes in plants is still difficult to achieve. Although a small proportion of commercial genetically modified (GM) crops present 'stacked' or 'pyramided' traits, only a handful of products have been developed by introducing three or more novel genes. On the research front, a variety of conventional and more novel methods have been employed to introduce multiple genes into plants, but all techniques suffer from certain drawbacks. In this review, the potential and problems of these various techniques and strategies are discussed, and the prospects for improving these technologies in the future are presented.

A short synthetic MAR positively affects transgene expression in rice and Arabidopsis

Matrix Attachment Regions (MARs) are DNA elements that are thought to influence gene expression by anchoring active chromatin domains to the nuclear matrix. When flanking a construct in transgenic plants, MARs could be useful for enhancing transgene expression. Naturally occurring MARs have a number of sequence features and DNA elements in common, and using different subsets of these sequence elements, three independent synthetic MARs were created. Although short, these MARs were able to bind nuclear scaffold preparations with an affinity equal to or greater than naturally occurring plant MARs. One synthetic MAR was extensively tested for its effect on transgene expression, using different MAR orientations, plant promoters, transformation methods and plant species. This MAR was able to increase average transgene expression and produced integration patterns of lower complexity. These data show the potential of making well defined synthetic MARs and using them to improve transgene expression.

Analysis of trans-silencing interactions using transcriptional silencers of varying strength and targets with and without flanking nuclear matrix attachment regions

We investigated the effect of the Rb7 matrix attachment region (MAR) on trans-silencing in tobacco plants, comparing the effects of three transgene silencer loci on ten target loci. Two of the silencer loci, C40 and C190, contain complex and rearranged transgene arrays consisting of 35S:GUS or NOS:NPTII containing plasmids. The third silencer locus, V271, was previously characterized as a complex locus containing rearranged 35S:RiN sequences. Each of these silencers can reduce 35S promoter-driven expression at other loci, albeit with varying efficiencies. The presence of MARs at a target locus does not prevent trans-silencing by the V271 silencer. However, four of seven MAR-containing loci were at least partially resistant to silencing by the C40 and C190 loci. One MAR locus was unaffected by C40, our weakest silencer, and three were silenced only when the silencer locus was maternally inherited. Silencing is progressive in the F1 and F2 generations; two days after germination there is little or no difference between seedlings derived from crosses to silencing or control lines, but seedlings containing silencer loci slowly lose expression during subsequent development. These observations are compatible with the hypothesis that a product of the silencer locus must accumulate before unlinked loci can be affected. However, our silencer loci are themselves silenced for GUS transcription, and coding region homology is not required for their effects on target loci. Our results are consistent with a model in which transcriptional silencing is triggered by transcription of sequences during the early stages of embryo or seedling development.

Functional analysis of two matrix attachment region (MAR) elements in transgenic maize plants

Matrix attachment regions (MARs) are binding sites for nuclear scaffold proteins in vitro, and are proposed to mediate the attachment of chromatin to the nuclear scaffold in vivo. Previous reports suggest that MAR elements may stabilize transgene expression. Here, we tested the effects of two maize MAR elements (P-MAR from the P1-rr gene, and Adh1-MAR from the adh1 gene) on the expression of a gusA reporter gene driven by three different promoters: the maize p1 gene promoter, a wheat peroxidase (WP) gene promoter, or a synthetic promoter (Rsyn7). The inclusion of P-MAR or Adh1-MAR on P::GUS transgene constructs did not reduce variation in the levels of GUS activity among independent transformation events, nor among the progeny derived from each event. The Adh1-MAR element did not affect GUS expression driven by the WP promoter, but did modify the spatial pattern of expression of the Rsyn7::GUS transgene. These results indicate that, in transgenic maize plants, the effects of MAR elements can vary significantly depending upon the promoter used to drive the transgene.

Assembly of two transgenes in an artificial chromatin domain gives highly coordinated expression in tobacco

The chromatin loop model predicts that genes within the same chromatin domain exhibit coordinated regulation. We here present the first direct experimental support for this model in plants. Two reporter genes, the E. coli beta-glucuronidase gene and the firefly luciferase gene, driven by different promoters, were placed between copies of the chicken lysozyme A element, a member of the matrix-associated region (MAR) group of chromatin boundary elements, and introduced in tobacco (Nicotiana tabacum). In plants carrying A elements, quantitative enzyme activities and mRNA levels of both genes show high correlations compared to control plants. The A element thus creates an artificial chromatin domain that yields coordinated expression. Surprisingly, enzyme activities correlated poorly with their respective mRNA levels. We hypothesize that this indicates the occurrence of "error pipelines" in data generation: systematic errors of a given analytical method will point in the same direction and cancel out in correlation analysis, resulting in better correlations. In combining different methods of analysis, however, such errors do not cancel out and as a result relevant correlations can be masked. Such error pipelines will have to be taken into account when different types of (e.g., whole-genome) data sets are combined in quantitative analyses.