Biological Significance of Unwinding Capability of Nuclear Matrix-Associating DNAs

Bode, Jürgen; Kohwi, Yoshinori; Dickinson, Liliane A.; Joh, Tadashi; Klehr, D.; Mielke, Christian; Kohwi‐Shigematsu, Terumi

doi:10.1126/science.1553545

Cited by 402 publications

(354 citation statements)

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“…We have identified A-box and T-box motifs (54), the yeast ARS consensus sequence (55), the consensus sequence for Drosophila topoisomerase II (7,73), the base unpairing region (BUR) (4,5,63,64), the MAR recognition sequence (MRS) (44), origin of replication and homeotic protein recognition motifs (ORI), TG-rich sequences, curved DNA motifs, and kinked DNA motifs (56,57,65,66,68). The frequency of occurrence of these motifs in each MAR is listed in Table 1.…”

Section: Resultsmentioning

confidence: 99%

“…DNA sequences that bestow a propensity for bending have been associated with MARs (62). A role for unwinding potential as a defining element for MARs has been suggested by Bode and co-workers (63). These workers have used a 9 bp sequence, the base-unpairing region (BUR), as a preliminary indicator of unwinding potential, but in collaboration with Benham (64) they have devised a much more sophisticated method of predicting stress-induced unwinding.…”

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confidence: 99%

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Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants^,

et al. 1999

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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 × 10 5 to 9 × 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.The idea that chromatin is organized into loop domains is as old as the original observation of loops in lampbrush chromosomes by Flemming in 1882 (1, 2). A reincarnation of that idea came from the electron micrographs of Paulson and Laemmli (3), which showed loops of DNA attached at their bases to the proteinaceous scaffold of metaphase chromosomes. A natural extension of the observations of Paulson and Laemmli is that the DNA-chromosome scaffold interaction is not random. Indeed, abundant evidence has been presented for interactions between specific DNA fragments and the metaphase chromosome scaffold and the interphase nuclear matrix [reviewed in Bode et al. (4,5)]. The specific DNA sequences have been termed MARs (matrix associated regions) (6) or SARs (scaffold attachment regions) (7,8). Both terms apparently describe the same biological entity (9). We use the term "MAR" because of its prevalence in the literature (10).MARs have a typical size of around 1 kb and have been postulated to form the anchorage points of torsionally constrained loop domains ranging in size from a few kb to more than 100 kb [reviewed by Gasser et al. (11) and Bode et al. (4,5)]. These putative structural elements of chromatin have attracted considerable attention because of evidence for their involvement in the regulation of transcription, including stabilization and increased levels of transgene expression (12)(13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27) [reviewed by Bode e...

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants^,

et al. 1999

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“…AT-rich sequences have been shown to possess strong nucleotide-unpairing properties [83], which may be involved in unzipping the DNA double helix during transcription initiation [84,85]. During eukaryotic interphase, chromosomes are organized into looped domains which are anchored to the nuclear matrix through DNA regions called matrix-attachment regions (MARs) [19,86].…”

Section: Classical Silencers (Silencer Elements)mentioning

confidence: 99%

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

Ogbourne

Antalis

1998

Biochemical Journal

223

171

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Mechanisms controlling transcription and its regulation are fundamental to our understanding of molecular biology and, ultimately, cellular biology. Our knowledge of transcription initiation and integral factors such as RNA polymerase is considerable, and more recently our understanding of the involvement of enhancers and complexes such as holoenzyme and mediator has increased dramatically. However, an understanding of transcriptional repression is also essential for a complete understanding of promoter structure and the regulation of gene expression. Transcriptional repression in eukaryotes is achieved through ‘silencers ’, of which there are two types, namely ‘silencer elements ’ and ‘negative regulatory elements ’ (NREs). Silencer elements are classical, position-independent elements that direct an active repression mechanism, and NREs are position-dependent elements that direct a passive repression mechanism. In addition, ‘repressors ’ are DNA-binding trasncription factors that interact directly with silencers. A review of the recent literature reveals that it is the silencer itself and its context within a given promoter, rather than the interacting repressor, that determines the mechanism of repression. Silencers form an intrinsic part of many eukaryotic promoters and, consequently, knowledge of their interactive role with enchancers and other transcriptional elements is essential for our understanding of gene regulation in eukaryotes.

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“…Recently, a small circular vector named pEPI-1 has been developed that is unique in that it can function as a stable episome without coding for any protein of viral origin. 16 This vector contains a chromosomal scaffold/matrix attachment region (S/MAR) deriving from the 5 0 -region of the human interferon b-gene, 17 as well as the origin of replication of the simian virus 40 genome (SV40 ori), the GFP cDNA driven by the CMV immediate-early promoter and the gene conferring resistance to neomycin. By transfer of pEPI-1 into CHO cells, it was shown that this vector replicates episomally over many cell generations in the absence of large T antigen.…”

Section: Introductionmentioning

confidence: 99%

Gene transfer into human hematopoietic progenitor cells with an episomal vector carrying an S/MAR element

et al. 2005

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Episomally maintained self-replicating systems present attractive alternative vehicles for gene therapy applications. Recent insights into the ability of chromosomal scaffold/ matrix attachment regions (S/MARs) to mediate episomal maintenance of genetic elements allowed the development of a small circular episomal vector that functions independently of virally encoded proteins. In this study, we investigated the potential of this vector, pEPI-eGFP, to mediate gene transfer in hematopoietic progenitor cell lines and primary human cells. pEPI-eGFP was episomally maintained and conferred sustained eGFP expression even in nonselective conditions in the human cell line, K562, as well as in primary human fibroblast-like cells. In contrast, in the murine erythroleukemia cell line, MEL, transgene expression was silenced through histone deacetylation, despite the vector's episomal persistence. Hematopoietic semisolid cell colonies derived from transfected human cord blood CD34 + cells expressed eGFP, albeit at low levels. After 4 weeks, the vector is retained in approximately 1% of progeny cells. Our results provide the first evidence that S/MAR-based plasmids can function as stable episomes in primary human cells, supporting long-term transgene expression. However, they do not display universal behavior in all cell types.

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Biological Significance of Unwinding Capability of Nuclear Matrix-Associating DNAs

Cited by 402 publications

References 38 publications

Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants^,

Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants^,

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

Gene transfer into human hematopoietic progenitor cells with an episomal vector carrying an S/MAR element

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Biological Significance of Unwinding Capability of Nuclear Matrix-Associating DNAs

Cited by 402 publications

References 38 publications

Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants,

Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants,

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

Gene transfer into human hematopoietic progenitor cells with an episomal vector carrying an S/MAR element

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Product

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Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants^,

Characterization of Randomly-Obtained Matrix Attachment Regions (MARs) from Higher Plants^,