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Validity of nuclear matrix

For a long time the question whether a polymer meshwork, a “nuclear matrix” or “nuclear-scaffold” or "NuMat" is an essential component of the in vivo nuclear architecture has remained a matter of debate. While there are arguments that the relative position of chromosome territories (CTs), the equivalent of condensed metaphase chromosomes at interphase, may be maintained due to steric hindrance or electrostatic repulsion forces between the apparently highly structured CT surfaces, this concept has to be reconciled with observations according to which cells treated with the classical matrix-extraction procedures maintain defined territories up to the point where a minor subset of acidic nuclear matrix proteins is released – very likely those proteins that governed their association with the nuclear skeleton.⁷ The nuclear matrix proteome consists of structural proteins, chaperones, DNA/RNA-binding proteins, chromatin remodeling and transcription factors. The complexity of NuMat is an indicator of diverse structural and functional significance of its proteins.⁸

Scaffold/Matrix attachment regions (S/MARs)

S/MARs (scaffold/matrix attachment regions), the DNA regions that are known to attach genomic DNA to variety of nuclear proteins, show an ever increasing spectrum of established biological activities. There is a known overlap of this large group of sequences with sequences termed LADs (lamina attachment domains).

S/MARs find increasing use for the rational design of vectors with widespread use in gene therapy and biotechnology. Nowadays S/MAR functions can be modulated, improved and custom-tailored to the specific needs of novel vector systems.⁹

Nuclear matrix and cancer

The nuclear matrix composition on human cells has been proven to be cell type and tumor specific. It has been clearly demonstrated that the nuclear matrix composition in a tumor is different from its normal counterparts.¹⁰ This fact could be useful to characterize cancer markers and to predict the disease even earlier. These markers have been found in urine and blood and could potentially be used in early detection and prognosis of human cancers.

See also

• Minicircle – Small, circular replicating units of DNA

Further reading

• Nickerson J (February 2001). "Experimental observations of a nuclear matrix". Journal of Cell Science. 114 (Pt 3): 463–74. doi:10.1242/jcs.114.3.463. PMID 11171316.
• Tsutsui KM, Sano K, Tsutsui K (August 2005). "Dynamic view of the nuclear matrix" (PDF). Acta Medica Okayama. 59 (4): 113–20. doi:10.18926/AMO/31953. PMID 16155636.
• Miller TE, Beausang LA, Winchell LF, Lidgard GP (January 1992). "Detection of nuclear matrix proteins in serum from cancer patients". Cancer Research. 52 (2): 422–7. PMID 1728414.
• Girod PA, Nguyen DQ, Calabrese D, Puttini S, Grandjean M, Martinet D, et al. (September 2007). "Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells". Nature Methods. 4 (9): 747–53. doi:10.1038/nmeth1076. PMID 17676049. S2CID 22315251.

References

1. Berezney, Ronald; Coffey, Donald S. (October 1974). "Identification of a nuclear protein matrix". Biochemical and Biophysical Research Communications. 60 (4): 1410–1417. doi:10.1016/0006-291X(74)90355-6. PMID 4214419. https://linkinghub.elsevier.com/retrieve/pii/0006291X74903556 ↩

2. Pederson T (March 2000). "Half a century of "the nuclear matrix"". Molecular Biology of the Cell. 11 (3): 799–805. doi:10.1091/mbc.11.3.799. PMC 14811. PMID 10712500. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC14811 ↩

3. ZBARSKII, I.B; DEBOV, S.S. (1948). "On the proteins of the cell nucleus". Dokl Akad Nauk SSSR. 63: 795–798. ↩

4. Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF (March 2006). "Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana". PLOS Computational Biology. 2 (3): e21. Bibcode:2006PLSCB...2...21T. doi:10.1371/journal.pcbi.0020021. PMC 1420657. PMID 16604187. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1420657 ↩

5. Hancock, Ronald (2000-07-05). "A new look at the nuclear matrix". Chromosoma. 109 (4): 219–225. doi:10.1007/s004120000077. ISSN 0009-5915. PMID 10968250. S2CID 8471350. http://link.springer.com/10.1007/s004120000077 ↩

6. Razin, S. V.; Borunova, V. V.; Iarovaia, O. V.; Vassetzky, Y. S. (July 2014). "Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus". Biochemistry (Moscow). 79 (7): 608–618. doi:10.1134/S0006297914070037. ISSN 0006-2979. PMID 25108324. S2CID 1678398. https://doi.org/10.1134%2FS0006297914070037 ↩

7. Hancock, Ronald (2000-07-05). "A new look at the nuclear matrix". Chromosoma. 109 (4): 219–225. doi:10.1007/s004120000077. ISSN 0009-5915. PMID 10968250. S2CID 8471350. http://link.springer.com/10.1007/s004120000077 ↩

8. Kallappagoudar S, Varma P, Pathak RU, Senthilkumar R, Mishra RK (September 2010). "Nuclear matrix proteome analysis of Drosophila melanogaster". Molecular & Cellular Proteomics. 9 (9): 2005–18. doi:10.1074/mcp.M110.001362. PMC 2938118. PMID 20530634. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938118 ↩

9. Bozza M, De Roia A, Correia MP, Berger A, Tuch A, Schmidt A, et al. (April 2021). "A nonviral, nonintegrating DNA nanovector platform for the safe, rapid, and persistent manufacture of recombinant T cells". Science Advances. 7 (16): eabf1333. Bibcode:2021SciA....7.1333B. doi:10.1126/sciadv.abf1333. PMC 8046366. PMID 33853779. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8046366 ↩

10. Rynearson AL, Sussman CR (June 2011). "Nuclear structure, organization, and oncogenesis". Journal of Gastrointestinal Cancer. 42 (2): 112–7. doi:10.1007/s12029-011-9253-5. PMID 21286858. S2CID 45830528. /wiki/Doi_(identifier) ↩