28:
279:. Episomes have the ability to divide together with the rest of eukaryotic genome during mitosis. Compared with standard plasmids they are not epigenetically silenced within nucleus and are not enzymatically destroyed. Episomes acquire this ability through the presence of S/MAR sequence within their construct.
297:
genes contain a significant higher portion of S/MARs. The pronounced difference in expression characteristics of S/MAR-containing genes emphasizes their functional importance and the importance of structural chromosomal characteristics for gene regulation in plants as well as within other eukaryotes.
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approaches support the idea that, by these properties, S/MARs not only separate a given transcriptional unit (chromatin domain) from its neighbors, but also provide platforms for the assembly of factors enabling transcriptional events within a given domain. An increased propensity to separate the DNA
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S/MAR-functions: constitutive and facultative. A chromatin domain with constitutive S/MARs at its termini (I). When functional demands require the specific translocation of the constituent gene to the matrix, facultative S/MARs responds to topological changes which are initiated by the association of
134:
and chromosome condensation. S/MARs do not have an obvious consensus sequence. Although prototype elements consist of AT-rich regions several hundred base pairs in length, the overall base composition is definitely not the primary determinant of their activity. Instead, their function requires a
238:
in 'all' cell types (whether or not the enclosed domain was transcribed), DNAse I hypersensitivity of the facultative type depended on the transcriptional status. The major difference between these two functional types of S/MARs is their size: the constitutive elements may extend over several
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has been estimated to approach 64,000 (chromatin domains) plus an additional 10,000 (replication foci), in 2007 still only a minor fraction (559 for all eukaryotes) had met the standard criteria for an annotation in the S/MARt database.
111:" or "nuclear-scaffold" is an essential component of eukaryotic nuclei. This nuclear skeleton acts as a dynamic support for many specialized events concerning the readout a spread of genetic information (see below).
233:
Subsequent work demonstrated both the constitutive (SAR-like) and the facultative (MAR-like) function of the elements depending on the context. Whereas constitutive S/MARs were found to be associated with a
37:. Topological changes are propagated once the gene is pulled through the transcriptional machinery (II). Transcription is terminated (III) followed by dissociation of the transcription complex (IV
95:. Studies on individual genes led to the conclusion that the dynamic and complex organization of the chromatin mediated by S/MAR elements plays an important role in the regulation of
376:
Cockerill PN, Garrard WT (January 1986). "Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites".
457:
Heng HH, Goetze S, Ye CJ, Liu G, Stevens JB, Bremer SW, et al. (March 2004). "Chromatin loops are selectively anchored using scaffold/matrix-attachment regions".
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Klar M, Stellamanns E, Ak P, Gluch A, Bode J (December 2005). "Dominant genomic structures: detection and potential signal functions in the interferon-beta domain".
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As an alternative to viral vectors, which can have unwanted effects in patients body, non-viral methods of gene therapy are being studied. One of such methods uses
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Mirkovitch J, Mirault ME, Laemmli UK (November 1984). "Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold".
293:. On a genome scale, pronounced tissue- and organ-specific and developmental expression patterns of S/MAR-containing genes have been detected. Notably,
229:(MARs) the first examples of which supported the immunoglobulin kapp-chain enhancer according to its occupancy with transcription factors
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adapts its structure and function to external signals. In retrospect it is of note that the discovery of S/MARs has two major routes:
122:(BCRs). Being association points for common nuclear structural proteins S/MARs are required for authentic and efficient chromosomal
578:"Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana"
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the fact that during transcription DNA is reeled through RNA-polymerase which itself is a fixed component of the nuclear matrix
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envision it as a dynamic entity, which changes its properties along the requirements of the cell nucleus—much the same as the
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the fact that certain domain-intrinsic S/MARs require the support of an adjacent transcription factor to become active.
633:
235:
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Jackson DA, Dolle A, Robertson G, Cook PR (August 1992). "The attachments of chromatin loops to the nucleoskeleton".
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The figure shows our present understanding of these properties and it incorporates the following findings:
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In 2006, Tetko found a strong correlation of intragenic S/MARs with spatiotemporal expression of genes in
175:
114:
S/MARs map to non-random locations in the genome. They occur at the flanks of transcribed regions, in 5´-
222:(SARs) by Laemmli and coworkers, which were thought to demarcate the borders of a given chromatin domain
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529:"Advances in the Development and the Applications of Nonviral, Episomal Vectors for Gene Therapy"
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kilobasepairs whereas facultative ones are at the lower size limit around 300 base pairs.
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Mulia GE, Picanço-Castro V, Stavrou EF, Athanassiadou A, Figueiredo ML (October 2021).
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pattern of "AT-patches" that confer the propensity for local strand unpairing under
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strands (the so-called 'stress induced duplex destabilization' potential,
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190:(cell type- and activity-related) depending on their dynamic properties.
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Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF (March 2006).
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It has been known for many years that a polymer meshwork, a so-called "
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for the chromatin scaffold and serve to organize the chromatin into
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within the nucleus. These elements constitute anchor points of the
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the dynamic properties of S/MAR-scaffold contacts as derived by
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186:(acting as permanent domain boundaries in all cell types) or
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attaches. As architectural DNA components that organize the
150:) can serve the formation of secondary structures such as
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apparatus). S/MARs have been classified as either being
158:, which are recognizable features for a number of
83:, S/MARs mediate structural organization of the
79:of eukaryotes into functional units within the
322:. Göttingen, Germany: University of Göttingen.
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33:transcription factors (TF) and supported by
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275:with special properties - the so-called
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7:
494:Cell Biology International Reports
193:While the number of S/MARs in the
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49:scaffold/matrix attachment region
67:), are sequences in the DNA of
1:
506:10.1016/s0309-1651(05)80013-x
172:poly(ADP-ribosyl) polymerases
595:10.1371/journal.pcbi.0020021
390:10.1016/0092-8674(86)90761-0
347:10.1016/0092-8674(84)90208-3
320:Department of Bioinformatics
220:scaffold-attachment elements
202:Context-dependent properties
236:DNase I hypersensitive site
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582:PLOS Computational Biology
436:10.1016/j.gene.2005.07.023
264:
120:breakpoint cluster regions
57:scaffold-attachment region
227:matrix-associated regions
225:the characterization of
65:matrix-associated region
459:Journal of Cell Science
283:Additional information
71:chromosomes where the
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206:Current views of the
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545:10.1089/hum.2020.310
539:(19–20): 1076–1095.
295:transcription factor
290:Arabidopsis thaliana
51:), otherwise called
261:Use in gene therapy
218:the description of
176:histone-acetylation
174:and enzymes of the
156:slippage structures
118:, and also at gene
35:histone acetylation
634:Molecular genetics
533:Human Gene Therapy
465:(Pt 7): 999–1008.
93:structural domains
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471:10.1242/jcs.00976
16:(Redirected from
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265:Main article:
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168:topoisomerases
143:Bioinformatics
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188:facultative
124:replication
588:(3): e21.
302:References
152:cruciforms
69:eukaryotic
430:: 79–89.
316:"SMARtDB"
85:chromatin
43:The term
628:Category
614:16604187
563:34348480
479:14996931
444:16185826
406:26202934
363:24634819
277:episomes
273:plasmids
248:haloFISH
103:Overview
605:1420657
554:8819515
514:1446346
398:3002631
355:6091913
267:Episome
160:enzymes
116:introns
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164:DNAses
130:, for
77:genome
59:), or
402:S2CID
359:S2CID
45:S/MAR
18:S/MAR
610:PMID
559:PMID
510:PMID
475:PMID
440:PMID
424:Gene
394:PMID
378:Cell
351:PMID
335:Cell
178:and
148:SIDD
126:and
600:PMC
590:doi
549:PMC
541:doi
502:doi
467:doi
463:117
432:doi
428:364
386:doi
343:doi
154:or
89:DNA
61:MAR
53:SAR
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