Skip to main content

Scaffold/Matrix Attachment Regions (S/MARs): Relevance for Disease and Therapy

  • Chapter
Protein-Protein Interactions as New Drug Targets

Part of the book series: Handbook of Experimental Pharmacology ((HEP,volume 186))

Abstract

There is increasing awareness that processes, such as development, aging and cancer, are governed, to a considerable extent, by epigenetic processes, such as DNA and histone modifications. The sites of these modifications in turn reflect their position and role in the nuclear architecture. Since epigenetic changes are easier to reverse than mutations, drugs that remove or add the chemical tags are at the forefront of research for the treatment of cancerous and inflammatory diseases. This review will use selected examples to develop a unified view that might assist the systematic development of novel therapeutic regimens.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • AK P, Benham C (2005) Susceptibility to superhelically driven DNA duplex destabilization: a highly preserved property of yeast replication origins. PloS Comput Biol 1:41–46

    Article  CAS  Google Scholar 

  • Albiez H, Cremer M, Tiberi C, Vecchio L, Schermelleh L, Dittrich S, Küpper K, Joffe B, Thormeyer T, von Hase J, Yang S, Rohr K, Leonhardt H, Solovei I, Cremer C, Fakan S, Cremer T (2006) Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosome Res 14:707–733

    Article  PubMed  CAS  Google Scholar 

  • 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 14:521–535

    PubMed  CAS  Google Scholar 

  • Alvarez-Gonzalez R, Watkins TA, Gill PK, Reed JL, Mendoza-Alvarez H (1999) Regulatory mechanisms of poly(ADP-ribose) polymerase. Mol Cell Biochem 19319–19322

    Google Scholar 

  • Antes TJ, Namicu SJ, Fournier REK, Levy-Wilson B (2001) The 5’-boundary of the human apolipoprotein B chromatin domain in intestinal cells. Biochemistry 40:6731–6742

    Article  PubMed  CAS  Google Scholar 

  • Bode J, Kohwi Y, Dickinson L, Joh T, Klehr D, Mielke C, Kohwi-Shigematsu T (1992) Biological significance of unwinding capability of nuclear matrix associating DNAs. Science 255:195–197

    Article  PubMed  CAS  Google Scholar 

  • Bode J, Schlake T, Rìos-Ramìrez M, Mielke C, Stengert M, Kay V, Klehr-Wirth D (1995) “Scaffold/matrix-attached regions: structural properties creating transcriptionally active loci”. In: Berezney R, Jeon KW (eds) International review of cytology 162A, on “Structural and Functional Organization of the Nuclear Matrix”, Academic Press, San Diego, pp 389–453

    Google Scholar 

  • Bode J, Stengert-Iber, M. Schlake T, Kay V, Dietz-Pfeilstetter A (1996) Scaffold/matrix-attached regions: topological switches with multiple regulatory functions. Crit Rev Eukaryot Gene Exp 6:115–138

    CAS  Google Scholar 

  • Bode J, Benham C, Ernst E, Knopp A, Marschalek R, Strick R, Strissel P (2000a) Fatal connections: when DNA ends meet on the nuclear matrix. J Cell Biochem Suppl 35:3–22

    Article  PubMed  Google Scholar 

  • Bode J, Benham C, Knopp A, Mielke C (2000b) Transcriptional augmentation: Modulation of gene expression by scaffold/matrix attached regions (S/MAR elements) Crit Rev Eukaryot Gene Exp 10:73–90

    CAS  Google Scholar 

  • Bode J, Fetzer CP, Nehlsen K, Scinteie M, Hinrich BH, Baiker A, Piechazcek C, Benham C, Lipps HJ (2001) The hitchhiking principle: Optimizing episomal vectors for the use in gene therapy and biotechnology. Gene Ther Mol Biol 6:33–46

    Google Scholar 

  • Bode J, Goetze S, Ernst E, Huesemann Y, Baer A, Seibler J, Mielke C (2003a) Architecture and utilization of highly-expressed genomic sites in “New Comprehensive Biochemistry 38”. In: Bernardi G (ed) Gene transfer and expression in mammalian cells, S. Makrides. Chap 20, Elsevier, Amsterdam, pp 551–572

    Chapter  Google Scholar 

  • Bode J, Goetze S, Heng H, Krawetz SA, Benham C (2003b) From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics. Chromosome Res 11(5):435–445

    Article  PubMed  CAS  Google Scholar 

  • Bode J, Winkelmann S, Goetze S, Spiker S, Tsutsui K, Bi C, AK P, Benham C (2006) Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy. J Mol Biol 358:597–613

    Article  PubMed  CAS  Google Scholar 

  • Branco MR, Pombo A (2006) Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations. PLoS Biol May 4(5):e138

    Article  CAS  Google Scholar 

  • Burke B, Stewart CL (2002) Life at the edge: the nuclear envelope and human disease. Nature Rev. Mol Cell Biol 3:575–585

    Article  CAS  Google Scholar 

  • Burke B, Stewart CL (2006) The laminopathies: the functional architecture of the nucleus and its contribution to disease. Ann Rev Genom Hum Genet 7:369–405

    Article  CAS  Google Scholar 

  • Bushmeyer SM, Atchison ML (1998) Identification of YY1 sequences necessary for association with the nuclear matrix and for transcriptional repression functions. J Cell Biochem 68:484–499

    Article  PubMed  CAS  Google Scholar 

  • Cai S, Han H, Kohwi-Shigematsu T (2003) Tissue-specific nuclear architecture and gene function regulated by a single protein SATB1. Nat Genet 34:42–51

    Article  PubMed  CAS  Google Scholar 

  • Chambon P, Weill JD, Mandel P (1963) Nicotinamide mononucleotide activation of newDNA-dependent polyadenylic acid synthesizing nuclear enzyme Biochem Biophys Res Commun 11:39–43

    Article  PubMed  CAS  Google Scholar 

  • Chang WJ, Alvarez-Gonzalez R (2001) The sequence-specific DNA binding of NF-kappa B is reversibly regulated by automodification-reaction of poly (ADP-ribose) polymerase 1. J Biol Chem 276:47664–47670

    Article  PubMed  CAS  Google Scholar 

  • Chen L, Lee L, Kudlow B, Dos Santos H, Sletvold O, Shafeghati Y, Botha E, Garg A, Hanson N, Martin G (2003) LMNA mutations in atypical Werner’s syndrome. Lancet 362:440–445

    Article  PubMed  CAS  Google Scholar 

  • D’Amours D, Desnoyers S, D’Silva I, Poirier GG (1999) Poly(ADP-ribosyl) ation reactions in the regulation of nuclear functions. Biochem J 342:249–268

    Article  PubMed  Google Scholar 

  • Deppert W (1996) Binding of MAR-DNA elements by mutant p53: possible implications for its oncogenic functions. J Cell Biochem 62:172–180

    Article  PubMed  CAS  Google Scholar 

  • Dobreva G, Chahrour M, Dautzenberg M, Chirivella L, Kanzler B, Fariñas I, Karsenty G, Grosschedl R (2003) SATB2 is a multifunctional determinant of craniofacial patterning and osteoblast differentiation. Cell 125:971–986

    Article  CAS  Google Scholar 

  • Fackelmayer FO (2004) Nuclear architecture and gene expression in the quest for novel therapeutics. Curr Pharmaceut Des 10:2851–2860

    Article  CAS  Google Scholar 

  • Faraone-Mennella MR (2005) Chromatin architecture and functions: the role(s) of poly(ADP-ribose) polymerase and poly(ADPribosyl) ation of nuclear proteins. Biochem Cell Biol 83(3):396–404

    Article  PubMed  CAS  Google Scholar 

  • Fey EG, Penman S (1988) Nuclear matrix proteins reflect cell type of origin in cultured human cells. Proc Natl Acad Sci USA 85:121–125

    Article  PubMed  CAS  Google Scholar 

  • Galande S (2002) Chromatin (dis) organization and cancer: BUR-binding proteins as biomarkers for cancer. Curr Cancer Drug Targets 2:157–190

    Article  PubMed  CAS  Google Scholar 

  • Galande S, Kohwi-Shigematsu T (1999) Poly(ADP-ribose) polymerase and Ku autoantigen form a complex and synergistically bind to matrix attachment sequences. J Biol Chem 27:20521–20528

    Article  Google Scholar 

  • Getzenberg RH (1994) The nuclear matrix and the regulation of gene expression: tissue specificity. J Cell Biochem 55(1):22–31

    Article  PubMed  CAS  Google Scholar 

  • Glazko GV, Koonin EV, Rogozin IB, Shabalina SA (2003) A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions. Trends Genet 19:119–124

    Article  PubMed  CAS  Google Scholar 

  • Goetze S, Gluch A, Benham C, Bode J (2003a) Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: the potential of predicting functional gene domains. Biochemistry 42:154–166

    Article  PubMed  CAS  Google Scholar 

  • Goetze S, Huesemann Y, Baer A, Bode J (2003b) Functional characterization of transgene integration patterns by Halo-FISH: electroporation versus retroviral infection. Biochemistry 42:7035–7043

    Article  PubMed  CAS  Google Scholar 

  • Goetze S, Baer A, Winkelmann S, Nehlsen K, Seibler J, Maass K, Bode J (2005) Genomic bordering elements: their performance at pre-defined genomic loci. Mol Cell Biol 25:2260–2272

    Article  PubMed  CAS  Google Scholar 

  • Griesenbeck J, Ziegler M, Tomilin N, Schweiger M, Oei SL (1999) Stimulation of the catalytic activity of poly(ADP-ribosyl) transferase by transcription factor Yin Yang 1. FEBS Lett 443:20–24

    Article  PubMed  CAS  Google Scholar 

  • Guo B, Odgren PR, van Wijnen AJ, Last TL, Nickerson J, Penman S, Lian JB, Stein JL, Stein GS (1995) The nuclear matrix protein NMP-1 is the transcription factor YY1. Proc Natl Acad Sci USA 92:10526–10530

    Article  PubMed  CAS  Google Scholar 

  • Hake SB, Xiao A, Allis CD (2004) Linking the epigenetic language of covalent histone modifications to cancer. Brit J Cancer 90:761–769

    Article  PubMed  CAS  Google Scholar 

  • Harborth J, Wang J, Gueth-Hallonet C, Weber K, Osborn M (1999) Self assembly of NuMA: multiarm oligomers as structural units of a nuclear lattice. EMBO J 18:1689–1700

    Article  PubMed  CAS  Google Scholar 

  • Heng HHQ, Goetze S, Ye CJ, Lu W, Liu G, Bremer S, Hughes M, Bode J, Krawetz SA (2004) Dynamic features of scaffold/matrix attached regions (S/MARs) in anchoring chromatin loops. J Cell Sci 17:999–1008

    Article  CAS  Google Scholar 

  • Henikoff S (2005) Histone modifications: Combinatorial complexity or cumulative simplicity? Proc Natl Acad Sci USA 102:5308–5309

    Article  PubMed  CAS  Google Scholar 

  • Hofmann WA, Stojiljkovic L, Fuchsova B, Vargas GM, Mavrommatis E, Philimonenko V, Kysela K, Goodrich JA, Lessard JL, Hope TJ, Hozak P, de Lanerolle P (2004) Actin is part of pre-initiation complexes and is necessary for transcription by RNA polymerase II. Nat Cell Biol 6:1094–1101

    Article  PubMed  CAS  Google Scholar 

  • Huber LJ, Chodosh LA (2005) Dynamics of DNA repair suggested by the subcellular localization of Brca1 and Brca2 proteins. J Cell Biochem 96:47–55

    Article  PubMed  CAS  Google Scholar 

  • Iarovaia OV, Bystritskiy A, Ravcheev D, Hancock R, Razin SV (2004) Visualization of individual DNA loops and a map of loop domains in the human dystrophin gene. Nucleic Acids Res 32:2079–2086

    Article  PubMed  CAS  Google Scholar 

  • Jackson D (2005) Understanding nuclear organization: when information becomes knowledge. EMBO Rep 6:213–217

    Article  PubMed  CAS  Google Scholar 

  • Jenke BH, Fetzer CP, Jönsson F, Fackelmayer FO, Conradt HC, Bode J, Lipps HJ (2001) An episomally replicating vector binds to the nuclear matrix protein SAF-A in vivo. EMBO Rep 3:349–354

    Article  Google Scholar 

  • Jiang M, Axea T, Holgate R, Rubbi CP, Okorokov AL, Mee T, Milner J (2001) p53 Binds the nuclear matrix in normal cells: binding involves the proline-rich domain of p53 and increases following genotoxic stress. Oncogene 20:5449–5458

    Article  PubMed  CAS  Google Scholar 

  • Johnson CN, Levy LS (2005) Matrix attachment regions as targets for retroviral integration. Virol J 2:68 doi:10.1186/1743–422X-2–68

    Article  PubMed  CAS  Google Scholar 

  • Ju BG, Lunyak VV, Perissi V, Garcia-Bassets I, Rose DW, Glass CK, Rosenfeld MGA (2006) Topoisomerase IIß-mediated dsDNA break required for regulated transcription. Science 312:1798–1802

    Article  PubMed  CAS  Google Scholar 

  • Kanda T, Sullivan KF, Wahl GM (1998) Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells. Curr Biol 8:377–385

    Article  PubMed  CAS  Google Scholar 

  • Kaplan MH, Zong RT, Herrscher RF, Scheuermann RH, Tucker PW (2001) Transcriptional activation by a matrix associating region-binding protein. J Biol Chem 276:21325–21330

    Article  PubMed  CAS  Google Scholar 

  • Kay V, Bode J (1994) Binding specificities of a nuclear scaffold: supercoiled, single stranded and SAR-DNA. Biochemistry 33:367–374

    Article  PubMed  CAS  Google Scholar 

  • Kay V, Bode J (1995) Detection of scaffold attached regions (SARs) by in vitro techniques; activities of these elements in vivo. In: Papavassiliou AG, King SL (eds) Methods in molecular and cellular biology: Methods for studying DNA protein interactions an overview, vol 5, Wiley Liss, Wilmington, pp 186–194

    Google Scholar 

  • Kim E, Deppert W (2004) Transcriptional activities of mutant p53: when mutations are more than a loss. J Cell Biochem 93:878–886

    Article  PubMed  CAS  Google Scholar 

  • Kipp M, Schwab BL, Przybylski M, Nicotera P, Fackelmayer FO (2000) Apoptotic cleavage of scaffold attachment factor A (SAF-A) by caspase-3 occurs at a noncanonical cleavage site. J Biol Chem 275:5031–5036

    Article  PubMed  CAS  Google Scholar 

  • Klar M, Bode J (2005) Enhanceosome formation over the interferon-beta promoter underlies a remote-control mechanism mediated by YY1 and YY2. Mol Cell Biol 25:10159–10170

    Article  PubMed  CAS  Google Scholar 

  • Kohwi-Shigematsu T, Maass K, Bode J (1997) A thymocyte factor, SATB1, suppresses transcription of stably integrated MAR linked reporter genes. Biochemistry 36:12005–12010

    Article  PubMed  CAS  Google Scholar 

  • Kramer JA, Zhang S, Yaron Y, Zhao Y, Krawetz SA (1997) Genetic testing for male infertility: a postulated role for mutations in sperm nuclear matrix attachment regions. Genetic Testing 1:125–129

    Article  PubMed  CAS  Google Scholar 

  • Kraus WLK, Lis JT (2003) PARP goes transcription. Cell 113:677–683

    Article  PubMed  CAS  Google Scholar 

  • Kukalev A, Nord Y, Palmberg C, Bergman T, Percipalle P (2005) Actin and hnRNP U cooperate for productive transcription by RNA polymerase II. Nat Struct Mol Biol 12:238–244

    Article  PubMed  CAS  Google Scholar 

  • Li B, Navarro S, Kasahara N, Comai L (2004) Identification and biochemical characterization of a Werner’s syndrome protein complex with Ku70/80 and poly(ADP-ribose) polymerase-1. J Biol Chem 279:13659–13667

    Article  PubMed  CAS  Google Scholar 

  • Liebich I, Bode J, Frisch M, Wingender E (2000) S/MARt DB-A database on scaffold/matrix attached regions. Nucleic Acids Res 30:372–374

    Article  Google Scholar 

  • Linnemann AK, Platts AE, Doggett N, Gluch A, Bode J, Krawetz SA (2007) Genome-wide identification of nuclear matrix attachment regions: an analysis of methods. Biochem Soc Trans 5:612–617

    Google Scholar 

  • Lipps HJ, Jenke ACW, Nehlsen K, Scinteie M, Stehle IM, Bode J (2003) Chromosome-based vectors for gene therapy. Gene 304:23–33

    Article  PubMed  CAS  Google Scholar 

  • Lonskaya I, Potaman VN, Shlyakhtenko LS, Oussatcheva EA, Lyubchenko YL, Soldatenkov VA (2006) Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding. J Biol Chem 280:17076–17083

    Article  CAS  Google Scholar 

  • Ludérus ME, de Graaf A, Mattia E, den Blaauwen JL, Grande MA, de Jong L, van Driel R (1992) Binding of matrix attachment regions to lamin B1. Cell 70:949–959

    Article  PubMed  Google Scholar 

  • Ludérus ME, den Blaauwen JL, de Smit OJ, Compton DA, van Driel R (1994) Binding of matrix attachment regions to lamin polymers involves single-stranded regions and the minor groove. Mol Cell Biol 14:6297–6305

    PubMed  Google Scholar 

  • 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 146:531–541

    Article  PubMed  CAS  Google Scholar 

  • Maniotis AJ, Bojanowski K, Ingeber DE (1997) Mechanical continuity and reversible chromosome disassembly within intact genomes removed from living cells. J Cell Biochem 65:114–130

    Article  PubMed  CAS  Google Scholar 

  • Martelli AM, Cocco L, Riederer BM, Neri LM (1996) The nuclear matrix: a critical appraisal. Histol Histopathol 11:1035–1048

    PubMed  CAS  Google Scholar 

  • Martelli AM, Falcieri EI, Zweyer M, Bortul R, Tabellini G, Capellini A, Cocco L, Moanzoli L (2002) The controversial nuclear matrix: a balanced point of view. Histol. Histopathol 17:1193–1205

    PubMed  CAS  Google Scholar 

  • Martens JHA, Verlaan M, Kalkhoven E, Dorsman JC, Zantema A (2002) Scaffold/matrix attachment region elements interact with a p300-scaffold attachment factor A complex and are bound by acetylated nucleosomes. Mol Cell Biol 22:2598–2606

    Article  PubMed  CAS  Google Scholar 

  • Martin-Oliva D, Aguilar-Quesada R, O’Valle F, Muñoz-Gámez JA, Martínez-Romero R, García del Moral R, Ruiz de Almodóvar JM, Villuendas R, Piris MA, Oliver FJ (2006) Inhibition of poly(ADP-ribose) polymerase modulates tumor-related gene expression, including hypoxia-inducible factor-1 activation, during skin carcinogenesis. Cancer Res 66:5744–5756

    Article  PubMed  CAS  Google Scholar 

  • Mattern KA, van Driel R, De Jong L (1997) Composition and structure of the internal nuclear matrix. In: Bird RC, Stein GS, Lian JB, Stein JL (eds) Nuclear structure and gene expression), Academic, New York, pp 87–110

    Chapter  Google Scholar 

  • McNeil S, Guo B, Stein JL, Lian JB, Bushmeyer S, Seto E, Atchinson ML, Penman S, van Wijnen AJ, Stein GS (1998) Targeting of the YY1 transcription factor to the nucleolus and the nuclear matrix in situ: the C-terminus is a principal determinant for nuclear trafficking. J Cell Biochem 68:500–510

    Article  PubMed  CAS  Google Scholar 

  • Mesner LD, Hamlin JL, Dijkwel PA (2003) The matrix attachment region in the Chinese hamster DHFR origin is dispensable for initiation of local chromatid separation. Proc Natl Acad Sci USA 100:3281–3286

    Article  PubMed  CAS  Google Scholar 

  • Mielke C, Kohwi Y, Kohwi-Shigematsu T, Bode J (1990) Hierarchical binding of DNA fragments derived from scaffold-attached regions: correlation of properties in vitro and Function in vivo. Biochemistry 29:7475–7485

    Article  PubMed  CAS  Google Scholar 

  • Mielke C, Maaß K, Tümmler M, Bode J (1996) Anatomy of highly-expressing chromosomal sites targeted by retroviral vectors. Biochemistry 35:2239–2252. Nakayasu H, Berezney R (1991) Nuclear matrins: Identification of the major nuclear matrix proteins. Proc Natl Acad Sci USA 88:10312–10316

    Article  PubMed  CAS  Google Scholar 

  • Nehlsen K, Broll S, Bode J (2006) Replicating minicircles: Generation of nonviral episomes for the efficient modification of dividing cells. Gene Ther Mol Biol 10:233–244

    Google Scholar 

  • Nobrega MA, Ovcharenko I, Afzal V, Rubin EM (2003) Scanning human gene deserts for long-range enhancers. Science 302:413

    Article  PubMed  CAS  Google Scholar 

  • Nobrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM (2004) Megabase deletions of gene deserts result in viable mice. Nature 431:988–993

    Article  PubMed  CAS  Google Scholar 

  • Oei SL, Shi Y (2001) Transcription factor Yin Yang 1 stimulates poly(ADP-ribosyl) ation and DNA repair. Biochem Biophys Res Commun 284:450–454

    Article  PubMed  CAS  Google Scholar 

  • Okorokov AL, Rubbi CP, Metcalfe S, Milner J (2002) The interaction of p53 with the nuclear matrix is mediated by F-actin and modulated by DNA damage. Oncogene 21:356–367

    Article  PubMed  CAS  Google Scholar 

  • Pederson T, Aebi U (2005) Nuclear actin extends, with no contraction in sight. Mol Cell Biol 16:5055–5060

    Article  CAS  Google Scholar 

  • Percipalle P, Jonsson A, Nashchekin D, Karlsson C, Bergman T, Guialis A, Daneholt B (2002) Nuclear actin is associated with a specific subset of hnRNP A/B-type proteins. Nucleic Acids Res 30:1725–1734

    Article  PubMed  CAS  Google Scholar 

  • Petrov A, Pirozhkova I, Carnac G, Laoudj D, Lipinski M, Vassetzky YS (2006) Chromatin loop domain organization within the 4q35 locus in facioscapulohumeral dystrophy patients versus normal human myoblasts. Proc Natl Acad Sci USA 103:6982–6987

    Article  PubMed  CAS  Google Scholar 

  • Replogle-Schwab TS, Getzenberg RH, Donat TL, Pienta KJ (1996) Effect of organ site on nuclear matrix protein composition. J Cell Biochem 62:132–141

    Article  PubMed  CAS  Google Scholar 

  • Rolli V, Ruf A, Augustin A, Schulz GE, Ménissier-de Murcia J, de Murcia G (2000) Poly(ADP-ribose) polymerase: structure and function. In: de Murcia G, Shall S (eds) From DNA damage and stress signalling to cell death: poly ADP-ribosylation reactions, Oxford University Press, New York, pp 35–79

    Google Scholar 

  • Scherrer K (1989) A unified matrix hypothesis of DNA-directed morphogenesis, protodynamism and growth control. Biosci Rep 9:157–188

    Article  PubMed  CAS  Google Scholar 

  • Schlake T, Klehr-Wirth D, Yoshida M, Beppu T, Bode J (1994) Gene expression within a chromatin domain: the role of core histone hyperacetylation. Biochemistry 33:4197–4206

    Article  PubMed  CAS  Google Scholar 

  • Schuebeler D, Mielke C, Maaß K, Bode J (1996) Scaffold/matrix-attached regions act upon transcription in a context-dependent manner. Biochemistry 35:11160–11169

    Article  CAS  Google Scholar 

  • Schwartz GH, Patnaik A, Hammond LA, Rizzo J, Berg K, Von Hoff DD, Rowinsky EK (2003) A phase I study of bizelesin, a highly potent and selective DNA-interactive agent, in patients with advanced solid malignancies. Ann Onc 14:775–782

    Article  CAS  Google Scholar 

  • Soldatenkov VA, Chasovskikh S, Potaman VN, Trofimova I, Smulson ME, Dritschilo A (2002) Transcriptional repression by binding of poly(ADP-ribose) polymerase to promoter sequences. J Biol Chem 277:665–670

    Article  PubMed  CAS  Google Scholar 

  • Straetling WH, Yu F (1999) Origin and roles of nuclear matrix proteins. Specific functions of the MAR-binding protein MeCP2/ARBP. Crit Rev Eukaryot Gene Exp 9:311–318

    Google Scholar 

  • Thomas CA (1971) The genetic organization of chromosomes. Ann Rev Genet 5:237–256

    Article  PubMed  CAS  Google Scholar 

  • Vendrely R, Vendrely C (1948) La teneur du noyau cellulaire en acide désoxyribonucléique à travers les organes, les individus et les espèces animales: techniques et premiers résultats. Experientia 4:434–436

    Article  PubMed  CAS  Google Scholar 

  • Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA et al (2001) The sequence of the human genome. Science 291:1304–1351

    Article  PubMed  CAS  Google Scholar 

  • Vidaković M, Grdovic, Quesada P, Bode J, Poznanović G (2004) Poly(ADP-ribose) polymerase-1: association with nuclear lamins in rat hepatocytes. J Cell Biochem 93:1155–1168

    Article  PubMed  CAS  Google Scholar 

  • Vidaković M, Koester M, Goetze S, Winkelmann S, Klar M, Poznanović G, Bode J (2005a). Colocalization of PARP-1 and lamin B in the nuclear architecture: a halo-fluorescence- and confocal microscopy study. J Cell Biochem 96:555–568

    Article  PubMed  CAS  Google Scholar 

  • Vidaković M, Poznanović G, Bode J (2005b) DNA break repair: Refined rules of an already complicated game. Biochem Cell Biol 83:365–373

    Article  PubMed  Google Scholar 

  • Virág L, Szabó C (2002) The therapeutic potential of poly(ADP-Ribose) polymerase inhibitors. Pharm Rev 54:375–429

    Article  PubMed  Google Scholar 

  • Vispé S, Yung TM, Ritchot J, Serizawa H, Satoh MS (2000) A cellular defense pathway regulating transcription through poly(ADP-ribosyl) ation in response to DNA damage. Proc Natl Acad Sci USA 97:9886–9891

    Article  PubMed  Google Scholar 

  • Wang Z, Goldstein A, Zong RT, Lin D, Neufeld EJ, Scheuermann RH, Tucker PW (1999) Cux/CDP homeoprotein is a component of NF-∝NR and represses the immunoglobulin heavy chain intronic enhancer by antagonizing the Bright transcription activator. Mol Cell Biol 19:284–295

    PubMed  CAS  Google Scholar 

  • Wen J, Huang S, Rogers, H. Dickinson LA, Kohwi-Shigematsu T, Noguchi CT (2005) SATB1 family protein expressed during early erythroid differentiation modifies globin gene expression. Blood 105:3330–3339

    Article  PubMed  CAS  Google Scholar 

  • Winkelmann S, Klar M, Benham C, AK P, Goetze S, Gluch A, Bode J (2006) The positive aspects of stress: strain initiates domain decondensation (SIDD). Brief Funct Genomic Proteomic 5:24–31

    Article  PubMed  CAS  Google Scholar 

  • Winkelmann S (2007) Dynamische Aspekte der Kernarchitektur: S/MARs und ihre Rolle bei der Etablierung aktiver Transkriptionseinheiten. Dissertation Technische Universität Braunschweig. http://www.digibib.tu-bs.de/?docid=00020961

  • Woynarowski JM, Trevino AV, Rodriguez KA, Hardies SC, Benham CJ (2001) AT-rich islands in genomic DNA as a novel target for AT-specific DNA-reactive antitumor drugs. J Biol Chem 276:40555–40566

    Article  PubMed  CAS  Google Scholar 

  • Zastrow MS, Vlcek S, Wilson KL (2004) Proteins that bind A-type lamins: integrating isolated clues. J Cell Sci 117:979–987

    Article  PubMed  CAS  Google Scholar 

  • Zbarsky IB, Debov SS (1948) On the proteins of the cell nuclei. Proc USSR Acad Sci 62:795–798

    Google Scholar 

  • Zeng C, He D, Brinkley BR (1994) Localization of NuMA protein isoforms in the nuclear matrix of mammalian cells. Cell Motil Cytoskel 29:167–176

    Article  CAS  Google Scholar 

  • Zeng C, van Wijnen AJ, Stein JL, Meyers S, Sun W, Shopland L, Lawrence JB, Penman S, Lian JB, Stein GS, Hiebert SW (1997) Identification of a nuclear matrix targeting signal in the leukemia and bone-related AML/CBF-alpha transcription factors. Proc Natl Acad Sci USA 6746–6751

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Gluch, A., Vidakovic, M., Bode, J. (2008). Scaffold/Matrix Attachment Regions (S/MARs): Relevance for Disease and Therapy. In: Klussmann, E., Scott, J. (eds) Protein-Protein Interactions as New Drug Targets. Handbook of Experimental Pharmacology, vol 186. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72843-6_4

Download citation

Publish with us

Policies and ethics