Transcriptional Modulation by Nuclear Matrix Protein P130/MAT3 Associated with MAR/SAR

  • Yasuhide Hibino
  • Tatsuhiro Usui
  • Koichi Hiraga


Various types of proteins are required for nuclear organization, which confers a variety of nuclear functions in eukaryotic cells. A set of proteins forms the chromosomal backbone (Paulson and Laemmli 1977) and different sets of proteins including chromatin-remodeling factors regulate the utilization of genetic code in chromosomal DNA (Boulikas 1995; Moazed 2001; Muchardt and Yaniv 2001). Eukaryotic chromosomes are topologically attached to the nuclear matrix (NM) or scaffold, a network of protein fibers referred to as the skeletal framework of the nucleus. The NM or scaffold is operationally defined as the residual structures that remain insoluble after extraction of nuclei with a high concentration of either salt or detergent. Several members of the group of proteins classified as components of the NM can directly bind to particular segments of chromosomal DNA. A DNA segment to which matrix and scaffold proteins can bind is termed a matrix or scaffold attachment region (MAR/SAR) (Cockerill and Garrard 1986; Gasser and Laemmli 1986; Cockerill et al. 1987; Jarman and Higgs 1988). One significant role of MAR/SARs that was revealed by structural analyses of the nucleus and chromosomes is the matrix- or scaffold-mediated stabilization of chromosomal structure. Chromosomal loops with an approximate length of ∼60 kilobases yield compact configurations of chromosomes.


Nuclear Matrix Chromosome Territory Nuclear Matrix Protein Protein MeCP2 Transcription Modulation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. Alvarez JD, Yasui DH, Niida H, Joh T, Loh DY, Kohwi-Shigematsu T (2000) The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development. Genes Dev 14:521–535PubMedGoogle Scholar
  2. Boulikas T (1995) Chromatin domains and prediction of MAR sequences. Int Rev Cytol 162A:279–388PubMedGoogle Scholar
  3. Boyes J, Bird A (1991) DNA methylation inhibits transcription indirectly via a methyl-CpG binding protein. Cell 64:1123–1134PubMedCrossRefGoogle Scholar
  4. Cai S, Han H-J, Kohwi-Shigematsu T (2003) Tissue-specific nuclear architecture and gene expression regulated by SATB1. Nat Genet 34:42–51PubMedCrossRefGoogle Scholar
  5. Chesnokov IN, Schmid CW (1995) Specific Alu binding protein from human sperm chromatin prevents DNA methylation. J Biol Chem 270:18539–18542PubMedCrossRefGoogle Scholar
  6. Cockerill PN, Garrard WT (1986) Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44:273–282PubMedCrossRefGoogle Scholar
  7. Cockerill PN, Yuen M-H, Garrard WT (1987) The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements. J Biol Chem 262:5394–5497PubMedGoogle Scholar
  8. Dickinson LA, Joh T, Kohwi Y, Kohwi-Shigematsu T (1992) A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell 70:631–645PubMedCrossRefGoogle Scholar
  9. Fackelmayer FO, Dahm K, Renz A, Ramsperger U, Richter A (1994) Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. Eur J Biochem 221:749–757PubMedCrossRefGoogle Scholar
  10. Forrester WC, van Genderen C, Jenuwein T, Grosschedl R (1994) Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions. Science 265:1221–1225PubMedCrossRefGoogle Scholar
  11. Fuks, F, Hurd PJ, Wolf D, Nan X, Bird AP, Kouzarides T (2003) The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J Biol Chem 278:4035–4040PubMedCrossRefGoogle Scholar
  12. Gasser SM, Laemmli UK (1986) Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46:521–530PubMedCrossRefGoogle Scholar
  13. Hagerman P J (1990) Sequence-directed curvature of DNA. Annu Rev Biochem 59:775–781CrossRefGoogle Scholar
  14. Hibino Y, Nakamura K, Tsukada S, Sugano N (1993) Purification and characterization of nuclear scaffold proteins which bind to a highly repetitive bent DNA from rat liver. Biochim Biophys Acta 1174:162–170PubMedGoogle Scholar
  15. Hibino Y, Ohzeki H, Hirose N, Morita Y, Sugano N (1998a) Involvement of DNA methylation in binding of a highly repetitive DNA component to nuclear scaffold proteins from rat liver. Biochem Biophys Res Commun 252:296–301PubMedCrossRefGoogle Scholar
  16. Hibino Y, Ohzeki H, Hirose N, Sugano N (1998b) Involvement of phosphorylation in binding of nuclear scaffold proteins from rat liver to a highly repetitive DNA component. Biochim Biophys Acta 1396:88–96PubMedGoogle Scholar
  17. Hibino Y, Ohzeki H, Sugano N, Hiraga K (2000) Transcription modulation by a rat nuclear scaffold protein, P130, and a rat highly repetitive DNA component or various types of animal and plant matrix or scaffold attachment regions. Biochem Biophys Res Commun 279:282–287PubMedCrossRefGoogle Scholar
  18. Ikeda Y, Nakamura K, Iwakami N, Hibino Y, Sugano N (1990) Base sequences of highly repetitive components in nuclear DNAs from rat liver and rat-ascites hepatoma. Cancer Lett 55:201–208PubMedCrossRefGoogle Scholar
  19. Jarman AP, Higgs DR (1988) Nuclear scaffold attachment sites in the human globin gene complexes. EMBO J 7:3337–3344PubMedGoogle Scholar
  20. Jenuwein T, Forrester WC, Fernández-Herrero LA, Laible G, Dull M, Grosschedl R (1997) Extension of chromatin accessibility by nuclear matrix attachment regions. Nature 385:269–272PubMedCrossRefGoogle Scholar
  21. Kohwi-Shigematsu T, Maass K, Bode J (1997) A thymocyte factor SATB1 suppresses transcription of stably integrated matrix-attachment region-linked reporter genes. Biochemistry 36:12005–12010PubMedCrossRefGoogle Scholar
  22. Li W, Chen HY, Davie JR (1996) Properties of chicken erythrocyte histone deacetylase associated with the nuclear matrix. Biochem J 314:631–637PubMedGoogle Scholar
  23. Ma H, Siegel AJ, Berezney R (1999) Association of chromosome territories with the nuclear matrix: disruption of human chromosome territories correlates with the release of a subset of nuclear matrix proteins. J Cell Biol 146:531–542PubMedCrossRefGoogle Scholar
  24. Martínez-Balbás A, Rodríguez-Campos A, García-Ramírez M, Sainz J, Carrera P, Aymamí J, Azorín F (1990) Satellite DNAs contain sequences that induce curvature. Biochemistry 29:2342–2348PubMedCrossRefGoogle Scholar
  25. Moazed D (2001) Common themes in mechanisms of gene silencing. Mol Cell 8:489–498PubMedCrossRefGoogle Scholar
  26. Muchardt C, Yaniv M (2001) When the SWI/SNF complex remodels.the cell cycle. Oncogene 20:3067–3075PubMedCrossRefGoogle Scholar
  27. Nan X, Campoy FJ, Bird A (1997) MeCP2 is a transcriptional repressor with abundant binding sites in genomic chromatin. Cell 88:471–481PubMedCrossRefGoogle Scholar
  28. Nan X, Ng H-H, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386–389PubMedCrossRefGoogle Scholar
  29. Nayler O, Strätling W, Bourquin JP, Stagljar I, Lindemann L, Jasper H, Hartmann AM, Fackelmayer FO, Ullrich A, Stamm S (1998) SAF-B protein couples transcription and pre-mRNA splicing to SAR/MAR elements. Nucleic Acids Res 26:3542–3549PubMedCrossRefGoogle Scholar
  30. Paulson JR, Laemmli UK (1977) The structure of histone-depleted metaphase chromosomes. Cell 12:817–828PubMedCrossRefGoogle Scholar
  31. Poljak L, Seum C, Mattioni T, Laemmli UK (1994) SARs stimulate but do not confer position independent gene expression. Nucleic Acids Res 22:4386–4394PubMedCrossRefGoogle Scholar
  32. Radic MZ, Lundgren K, Hamkalo BA (1987) Curvature of mouse satellite DNA and condensation of heterochromatin. Cell 50:1101–1108PubMedCrossRefGoogle Scholar
  33. Razin SV, Mantieva VL, Georgiev GP (1979) The similarity of DNA sequences remaining bound to scaffold upon nuclease treatment of interphase nuclei and metaphase chromosomes. Nucleic Acids Res 7:1713–1735PubMedCrossRefGoogle Scholar
  34. Romig H, Fackelmayer FO, Renz A, Ramsperger U, Richter A (1992) Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. EMBO J 11:3431–3440PubMedGoogle Scholar
  35. Shrader TE, Crothers DM (1990) Effects of DNA sequence and histone-histone interactions on nucleosome placement. J Mol Biol 216:69–84PubMedCrossRefGoogle Scholar
  36. Singer MF (1982) Highly repeated sequences in mammalian genomes. Int Rev Cytol 76:67–112PubMedCrossRefGoogle Scholar
  37. Small D, Nelkin B, Vogelstein B (1982) Nonrandom distribution of repeated DNA sequences with respect to supercoiled loops and the nuclear matrix. Proc Natl Acad Sci USA 79:5911–5915PubMedCrossRefGoogle Scholar
  38. Weitzel JM, Buhrmester H, Strätling WH (1997) Chicken MAR-binding protein ARBP is homologous to rat methyl-CpG-binding protein MeCP2. Mol Cell Biol 17:5656–5666PubMedGoogle Scholar
  39. Xu M, Hammer RE, Blasquez VC, Jones SL, Garrard WT (1989) Immunoglobulin kappa gene expression after stable integration. II. Role of the intronic MAR and enhancer in transgenic mice. J Biol Chem 264:21190–21195PubMedGoogle Scholar
  40. Zink D, Cremer T, Saffrich R, Fischer R, Trendelenburg MF, Ansorge W, Stelzer EH (1998) Structure and dynamics of human interphase chromosome territories in vivo. Hum Genet 102:241–251PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Yasuhide Hibino
    • 1
  • Tatsuhiro Usui
    • 1
  • Koichi Hiraga
    • 2
  1. 1.Department of Clinical Dietetics and Human Nutrition, Faculty of Pharmaceutical SciencesJosai UniversitySakado, SaitamaJapan
  2. 2.Department of Biochemistry, School of MedicineToyama UniversityToyamaJapan

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