@article{francis_spiker_2005, title={Identification of Arabidopsis thaliana transformants without selection reveals a high occurrence of silenced T-DNA integrations}, volume={41}, ISSN={["0960-7412"]}, DOI={10.1111/j.1365-313X.2004.02312.x}, abstractNote={Summary}, number={3}, journal={PLANT JOURNAL}, author={Francis, KE and Spiker, S}, year={2005}, month={Feb}, pages={464–477} }
 @article{halweg_thompson_spiker_2005, title={The rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: A flow cytometric study}, volume={17}, ISSN={["1532-298X"]}, DOI={10.1105/tpc.104.028100}, abstractNote={Many studies in both plant and animal systems have shown that matrix attachment regions (MARs) can increase expression of transgenes in whole organisms or cells in culture. Because histochemical assays often indicate variegated transgene expression, a question arises: Do MARs increase transgene expression by increasing the percentage of cells expressing the transgene (likelihood), by increasing the level of expression in expressing cells (magnitude), or both? To address this question, we used flow cytometry to measure green fluorescent protein (GFP) expression in individual tobacco (Nicotiana tabacum) cells from lines transformed by Agrobacterium tumefaciens. We conclude that MAR-mediated overall increases in transgene expression involve both likelihood and magnitude. On average, cell lines transformed with the Rb7 MAR-containing vector expressed GFP at levels 2.0- to 3.7-fold higher than controls. MAR lines had fewer nonexpressing cells than control lines (10% versus 45%), and the magnitude of GFP expression in expressing cells was greater in MAR lines by 1.9- to 2.9-fold. We also show that flow cytometry measurements on cells from isogenic lines are consistent with those from populations of independently transformed cell lines. By obviating the need to establish isogenic lines, this use of flow cytometry could greatly simplify the evaluation of MARs or other sequence elements that affect transgene expression.}, number={2}, journal={PLANT CELL}, author={Halweg, C and Thompson, WF and Spiker, S}, year={2005}, month={Feb}, pages={418–429} }
 @article{busov_johannes_whetten_sederoff_spiker_lanz-garcia_goldfarb_2004, title={An auxin-inducible gene from loblolly pine ( Pinus taeda L.) is differentially expressed in mature and juvenile-phase shoots and encodes a putative transmembrane protein}, volume={218}, ISSN={0032-0935 1432-2048}, url={http://dx.doi.org/10.1007/s00425-003-1175-4}, DOI={10.1007/s00425-003-1175-4}, abstractNote={We have isolated a gene from loblolly pine, 5NG4, that is highly and specifically induced by auxin in juvenile loblolly pine shoots prior to adventitious root formation, but substantially down-regulated in physiologically mature shoots that are adventitious rooting incompetent. 5NG4 was highly auxin-induced in roots, stems and hypocotyls, organs that can form either lateral or adventitious roots following an auxin treatment, but was not induced to the same level in needles and cotyledons, organs that do not form roots. The deduced amino acid sequence shows homology to the MtN21 nodulin gene from Medicago truncatula. The expression pattern of 5NG4 and its homology to a protein from Medicago involved in a root-related process suggest a possible role for this gene in adventitious root formation. Homology searches also identified similar proteins in Arabidopsis thaliana and Oryza sativa. High conservation across these evolutionarily distant species suggests essential functions in plant growth and development. A 38-member family of genes homologous to 5NG4 was identified in the A. thaliana genome. The physiological significance of this redundancy is most likely associated with functional divergence and/or expression specificity of the different family members. The exact biochemical function of the gene is still unknown, but sequence and structure predictions and 5NG4::GFP fusion protein localizations indicate it is a transmembrane protein with a possible transport function.}, number={6}, journal={Planta}, publisher={Springer Science and Business Media LLC}, author={Busov, Victor B. and Johannes, Eva and Whetten, Ross W. and Sederoff, Ronald R. and Spiker, Steven L. and Lanz-Garcia, Carmen and Goldfarb, Barry}, year={2004}, month={Apr}, pages={916–927} }
 @article{mankin_allen_phelan_spiker_thompson_2003, title={Elevation of transgene expression level by flanking matrix attachment regions (MAR) is promoter dependent: a study of the interactions of six promoters with the RB7 3 ' MAR}, volume={12}, ISSN={["0962-8819"]}, DOI={10.1023/A:1022194120518}, abstractNote={We have analyzed effects of a matrix attachment region (MAR) from the tobacco RB7 gene on transgene expression from six different promoters in stably transformed tobacco cell cultures. The presence of MARs flanking the transgene increased expression of constructs based on the constitutive CaMV 35S, NOS, and OCS promoters. Expression from an induced heat shock promoter was also increased and MARs did not cause expression in the absence of heat shock. There was also no effect of MARs on the pea ferredoxin promoter, which is not normally expressed in this cell line. Importantly, most transgenes flanked by RB7 MAR elements showed a large reduction in the number of low expressing GUS transformants relative to control constructs without MARs.}, number={1}, journal={TRANSGENIC RESEARCH}, author={Mankin, SL and Allen, GC and Phelan, T and Spiker, S and Thompson, WF}, year={2003}, month={Feb}, pages={3–12} }
 @article{ulker_weissinger_spiker_2002, title={E-coli chromosomal DNA in a transgene locus created by microprojectile bombardment in tobacco}, volume={11}, ISSN={["0962-8819"]}, DOI={10.1023/A:1015614220200}, number={3}, journal={TRANSGENIC RESEARCH}, author={Ulker, B and Weissinger, AK and Spiker, S}, year={2002}, month={Jun}, pages={311–313} }
 @misc{mendu_massel_spiker_2001, title={Increasing loop domain size does not diminish effects of matrix attachment regions on transgene expression in tobacco cells in culture}, volume={496}, ISSN={["0014-5793"]}, DOI={10.1016/s0014-5793(01)02406-1}, abstractNote={It is now widely held that the chromatin of eukaryotic organisms is organized into loop domains in which chromatin fibers are attached to the nuclear matrix by specific interactions of nuclear matrix proteins with DNA sequences called matrix attachment regions (MARs) [1, 2]. Several MARs have been isolated and incorporated into constructs used for transformation. Work with animal cell culture systems has consistently shown much higher average levels of reporter gene expression in cell lines in which reporter genes are flanked with cloned MARs than in control lines without flanking MARs [1]. MARs have similar effects in plant cell systems. For example, in a tobacco cell culture system, we have shown that a heterologous MAR (a yeast MAR that binds weakly to the tobacco nuclear matrix) increases reporter gene expression by 12-fold, and a strong matrix-binding tobacco MAR increases reporter gene expression by 60-fold [3]. The mechanisms by which MARs increase reporter gene expression are unknown. MARs do not appear to act as typical enhancers, as they have little effect in transient expression assays [1, 2]. Most proposed mechanisms involve chromatin structure [1, 2]. According to one model, MARs affect transgene expression by creating independent, topologically isolated domains. The transgenes in these independent domains are insulated from chromatin structure of the native domains (either transcriptionally active or repressed) into which they become incorporated. If transgenic MARs do act by creating independent domains containing the transgene, the question remains of why the independent domains have a transcriptionally active chromatin structure. We have previously speculated that independent domains created by cloned MARs may have transcriptionally active chromatin structures because they are too small to form stable, transcriptionally repressed, condensed chromatin fibers in vivo [2, 3]. In our previous experiments, the putative domain formed by cloned MARs contains 3 kb of DNA, enough to form 16 plant nucleosomes. Even fewer nucleosomes may form on the transgenes in vivo, as close proximity to the nuclear matrix may sterically inhibit nucleosome formation. As the structure of the 30-nm chromatin fiber is not well understood, the number of nucleosomes necessary to form a stable, transcriptionally repressed structure is unknown. Formation of folded chromatin fibers presumably is dependent upon nucleosome–nucleosome interactions. If we consider the solenoid model of the 30-nm fiber (six nucleosomes per turn of the solenoid), it is logical to assume that a minimum of 12 nucleosomes would be required to form a stable, folded structure. This would allow each nucleosome to interact with at least one nucleosome other than its linear neighbors. Further turns of the solenoid would be expected to further stabilize the structure. For example, in a structure containing 18 nucleosomes (three turns of the solenoid), the nucleosomes of the middle turn could interact with nucleosomes of the outside two turns of the solenoid. Carruthers et al. [4] have provided evidence that a reconstituted linear DNA fragment containing 12 nucleosomes can form a stable, folded structure, but the relationship of this structure to the 30-nm fiber is unclear. The work of Butler and Thomas [5] indicates that more nucleosomes may be required. These workers observed a change in the hydrodynamic properties of native, rat liver nucleosome oligomers above the size of 50 nucleosomes. They attributed the change to higher-order folding. The considerations mentioned above suggest that in our previous work [2, 3] the 16 nucleosomes that would be expected to form on 3 kb of DNA bounded by MARs may be below or near the minimum required to form stable, folded chromatin fibers in vivo. Based on these ideas concerning the stability of higher-order structure in chromatin, we have asked if the enhancement of transgene expression by MARs can be counteracted by increasing the amount of DNA in the putative loop domain to a point at which a stable condensed chromatin fiber could be formed. In order to answer this question we have transformed plant cells in culture by microprojectile bombardment as we have previously described [3]. A co-transformation procedure is used in which a selectable marker (NPTII conferring kanamycin resistance) is carried on a separate plasmid from the reporter gene. As in our previous experiments we have used the reporter plasmids, pGHNC11 and pGHNC12 (Fig. 1A ). These plasmids contain the GUS reporter gene cassette flanked by the RB7-6 tobacco MAR and a control of the GUS cassette without flanking MARs. We also used a plasmid (pNMCS1 in Fig. 1A) in which λ DNA has been inserted between the GUS reporter cassette and the MAR. This ‘spacer’ DNA would increase the size of the putative MAR-bounded loop domain to 52 nucleosomes. The λ DNA (a 6.6-kb HindIII fragment, nucleotides 37586–44141) has an AT content of 51% and does not bind to the tobacco nuclear matrix (data not shown). A control plasmid (pNMCS2) with the λ DNA and the GUS reporter cassette but no MARs was also used. Kanamycin-resistant transformed cells were grown in liquid culture for 2 months with transfers every 7 days. At this time, cells were harvested and protein extracts were made in order to measure GUS specific activity [3]. Fig. 1B shows the results of the GUS specific activity measurements. Increasing the amount of DNA in the putative independent domain to a size that would support 8.6 turns of a nucleosome solenoid does not diminish the effect of MARs on enhancing reporter gene expression. The specific activity of the MAR-SPACER-GUS-MAR transformed cell lines is slightly higher than that in the MAR-GUS-MAR lines, but the difference is not statistically significant. In the lines transformed with constructs lacking MARs, the GUS activity was slightly lower in the SPACER-GUS lines than in the GUS-only lines, but again, this difference was not statistically significant. Because most DNA constructs used to test the effects of MARs on transgene expression contain amounts of DNA between the MARs that would be sufficient to form only a few nucleosomes [1-3], we hypothesized that the mechanism of MAR activity is the formation of loop domains that are too small to form a stable, transcriptionally repressed chromatin fiber. Increasing the amount of DNA in the putative MAR-bounded loop domains to a size that would accommodate 52 nucleosomes (nearly nine turns of a nucleosome solenoid) does not diminish the MAR-mediated enhancement of transgene expression in tobacco cells in culture. In vitro data indicate that 52 nucleosomes would be more than enough to support a stable, condensed chromatin fiber [5]. Thus, the explanation for MAR enhancement of transgene expression must lie elsewhere. We also note that the 5′ MAR is able to influence transgene expression at a fairly great distance (at least 6.6 kb from the promoter). It could be argued that the MAR located 3′ to the transgene is by itself causing the enhancement of transgene expression. But we have previously shown [2, 3] that both 5′ and 3′ flanking MARs are necessary to get the full MAR effect on increasing transgene expression. This work was supported by grant 9418491 from the USA National Science Foundation and by the North Carolina State University Agricultural Research Service.}, number={1}, journal={FEBS LETTERS}, author={Mendu, N and Massel, M and Spiker, S}, year={2001}, month={May}, pages={66–67} }
 @misc{michalowski_spiker_2001, title={Matrix attachment regions}, volume={6,245,974}, number={2001 June 12}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Michalowski, S. M. and Spiker, S.}, year={2001} }
 @article{ascenzi_ingram_massel_thompson_spiker_weissinger_2001, title={The role of cell differentiation state and HMG-I/Y in the expression of transgenes flanked by matrix attachment regions}, volume={10}, ISSN={["0962-8819"]}, DOI={10.1023/A:1012082602587}, abstractNote={The tobacco nuclear matrix attachment region (MAR), RB7, has been shown to have a much greater effect on transgene expression in cultured cells than in transgenic plants. This is comparable to work in mouse systems showing that MARs have a positive effect on transgene expression in embryonic tissues but not adult tissues. There are several possible explanations for these observations. One is that cell differentiation state and proliferation rate can affect MAR function. We tested this possibility by initiating suspension cell cultures from well-characterized transgenic plants transformed with 35S::GUS with and without flanking MARs and then comparing GUS specific activity in the cell lines to those of the transgenic plants from which the cell lines were derived. If cell differentiation state and proliferation rate do affect MAR function, we would expect the ratio of transgene expression (cell suspensions : plants) to be greater in MAR lines than in control lines. This turned out not to be the case. Thus, it appears that MAR function is not enhanced simply because cells in culture divide rapidly and are not differentiated. Because in animal systems the chromosomal protein HMG-I/Y has been shown to be upregulated in proliferating cells and may have a role in MAR function, we have also examined the levels of the tobacco HMG-I/Y homolog by immunoblotting. The level of this protein does not differ between primary transformant cultured cells (NT-1) and Nicotiana tabacum plants (SR-1). However, a higher molecular weight cross-reacting polypeptide was found in nuclei from the NT-1 cell suspensions but was not detected in SR-1 leaf nuclei or cell suspensions derived from the SR-1 plants.}, number={5}, journal={TRANSGENIC RESEARCH}, author={Ascenzi, R and Ingram, JL and Massel, M and Thompson, WF and Spiker, S and Weissinger, AK}, year={2001}, pages={465–470} }
 @misc{allen_spiker_thompson_2000, title={Use of matrix attachment regions (MARs) to minimize transgene silencing}, volume={43}, ISSN={["0167-4412"]}, DOI={10.1023/A:1006424621037}, abstractNote={Matrix attachment regions (MARs) are operationally defined as DNA elements that bind specifically to the nuclear matrix in vitro. It is possible, although unproven, that they also mediate binding of chromatin to the nuclear matrix in vivo and alter the topology of the genome in interphase nuclei. When MARs are positioned on either side of a transgene their presence usually results in higher and more stable expression in transgenic plants or cell lines, most likely by minimizing gene silencing. Our review explores current data and presents several plausible models to explain MAR effects on transgene expression.}, number={2-3}, journal={PLANT MOLECULAR BIOLOGY}, author={Allen, GC and Spiker, S and Thompson, WF}, year={2000}, month={Jun}, pages={361–376} }
 @article{ulker_allen_thompson_spiker_weissinger_1999, title={A tobacco matrix attachment region reduces the loss of transgene expression in the progeny of transgenic tobacco plants}, volume={18}, ISSN={["1365-313X"]}, DOI={10.1046/j.1365-313X.1999.00453.x}, abstractNote={Summary}, number={3}, journal={PLANT JOURNAL}, author={Ulker, B and Allen, GC and Thompson, WF and Spiker, S and Weissinger, AK}, year={1999}, month={May}, pages={253–263} }
 @article{michalowski_allen_hall_thompson_spiker_1999, title={Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants}, volume={38}, ISSN={["0006-2960"]}, DOI={10.1021/bi991142c}, abstractNote={Matrix attachment regions (MARs) can be operationally defined as DNA fragments that bind to the nuclear matrix. We have created a library of randomly obtained MARs from tobacco (Nicotiana tobacum) by cloning DNA fragments that co-isolate with nuclear matrixes prepared by a method involving lithium diiodosalicylate. The interactions of several of the cloned MARs with nuclear matrixes were tested by an in vitro binding assay in which genomic DNA was used as competitor. Based on this assay, the MARs were classified as strong, medium, and weak binders. Examples of each of the binding classes were further studied by in vitro binding using self- and cross-competition. Estimates of dissociation constants for several MARs ranged from 6 to 11 nM and correlated inversely with binding strength. The number of binding sites per matrix for several MARs ranged from 4 x 10(5) to 9 x 10(5) and correlated directly with binding strength. We conclude that binding strength, as we have measured it, is a function of both numbers of binding sites and affinity for the sites. The tobacco MARs were sequenced and analyzed for overall AT content, for distribution of AT-rich regions, and for the abundance of several MAR-related motifs. Previously identified MAR motifs correlate to various degrees with binding strength. Notably, the Drosophila topoisomerase II motif does not correlate with binding strength of the tobacco MARs. A newly identified motif, the "90%AT Box," correlates better with binding strength than any of the previously identified motifs we investigated.}, number={39}, journal={BIOCHEMISTRY}, author={Michalowski, SM and Allen, GC and Hall, GE and Thompson, WF and Spiker, S}, year={1999}, month={Sep}, pages={12795–12804} }
 @misc{method of increasing expression for foreign genes in plant cells_1998, volume={5,773,689}, number={1998 June 30}, publisher={Washington, DC: U.S. Patent and Trademark Office}, year={1998} }
 @misc{plant nuclear scaffold attachment region and method for increasing gene expression in transgenic cells_1998, volume={5,773,695}, number={1998 June 30}, publisher={Washington, DC: U.S. Patent and Trademark Office}, year={1998} }
 @article{iglesias_moscone_papp_neuhuber_michalowski_phelan_spiker_matzke_matzke_1997, title={Molecular and cytogenetic analyses of stably and unstably expressed transgene loci in tobacco}, volume={9}, ISSN={["1040-4651"]}, DOI={10.1105/tpc.9.8.1251}, abstractNote={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.}, number={8}, journal={PLANT CELL}, author={Iglesias, VA and Moscone, EA and Papp, I and Neuhuber, F and Michalowski, S and Phelan, T and Spiker, S and Matzke, M and Matzke, AJM}, year={1997}, month={Aug}, pages={1251–1264} }
 @article{meier_groning_michalowski_spiker_1997, title={The tomato RBCS3A promoter requires integration into the chromatin for correct organ-specific regulation}, volume={415}, ISSN={["0014-5793"]}, DOI={10.1016/S0014-5793(97)01102-2}, abstractNote={In tomato, the RBCS1, RBCS2 and RBCS3A genes, encoding the small subunit of ribulose‐1,5‐bisphosphate carboxylase/oxygenase, are expressed in leaves and light‐grown seedlings, but only RBCS1 and RBCS2 are expressed in developing tomato fruits. The activities of the three promoters have been compared in transgenic plants and after transient transformation. Fruit‐specific repression of the RBCS3A promoter was observed in transgenic plants, but not after ballistic transient transformation, indicating that chromatin integration is necessary for its correct organ‐specific regulation. In addition, matrix attachment regions have been identified in the RBCS1, RBCS2 and RBCS3A promoters. This is the second case in plants of absence of correct regulation of a plasmid‐borne plant promoter and correlating potential nuclear matrix attachment of the gene.}, number={1}, journal={FEBS LETTERS}, author={Meier, I and Groning, B and Michalowski, S and Spiker, S}, year={1997}, month={Sep}, pages={91–95} }
 @article{spiker_thompson_1996, title={Nuclear Matrix Attachment Regions and Transgene Expression in Plants}, volume={110}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.110.1.15}, DOI={10.1104/pp.110.1.15}, abstractNote={DNA sequences called matrix attachment regions (MARs) or scaffold attachment regions (SARs) have recently attracted much attention because of their perceived capacity to increase levels of transgene expression and reduce transformant-to-transformant variation of transgene expression in both plants and animals. Work with these sequences is in its early stages and data that seem to be contradictory have been presented. We do not intend to resolve these controversies here (this will be accomplished by further research). Rather, we will discuss the hypothesized role of MARs in chromatin structure, how MARs are isolated and characterized, what effects MARs have had on the expression of transgenes and the models that have been evoked to explain those effects.}, number={1}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Spiker, S. and Thompson, W. F.}, year={1996}, month={Jan}, pages={15–21} }