Biopolym. Cell. 2009; 25(6):451-456.
Structure and Function of Biopolymers
MARs Wars: heterogeneity and clustering of DNA-binding domains in the nuclear matrix
1, 2Vassetzky Y. S., 3Ioudinkova E. S., 3Razin S. V.
  1. CNRS UMR 8126, Univ. Paris-Sud 11, Institut Gustave Roussy
    39, Camille-Desmoulins Str., 94805 Villejuif, France
  2. N. K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences
    26, Vavilova Str., Moscow, Russian Federation, 119334
  3. Institute of Gene Biology, Russian Academy of Sciences
    34/5, Vavilova Str., Moscow, Russian Federation, 119334


Aim. CO326 is a chicken nuclear scaffold/matrix attachment region (MAR) associated with the nuclear matrix in several types of chicken cells. It contains a binding site for a sequence-specific DNA-binding protein, F326. We have studied its interaction with the nuclear matrix. Methods. We have used an in vitro MAR assay with isolated matrices from chicken HD3 cells. Results. We have found that an oligonucleotide binding site for the F326 inhibits binding of the CO326 to the nuclear matrix. At the same time, the binding of heterologous MARs is enhanced. Conclusions. Taken together, these data suggest that there exist several classes of MARs and MAR-binding domains and that the MAR-binding proteins may be clustered in the nuclear matrix.
Keywords: nuclear matrix, DNA-protein interactions, MAR, SAR


[1] Vassetzky Y., Lemaitre J. M., Mechali M. Specification of chromatin domains and regulation of replication and transcription during development Crit. Rev. Eukaryot. Gene Exp 2000 10, N 1:31–38.
[2] Razin S. V., Iarovaia O. V., Sjakste N., Sjakste T., Bagdoniene L., Rynditch A. V., Eivazova E. R., Lipinski M., Vassetzky Y. S. Chromatin domains and regulation of transcription J. Mol. Biol 2007 369, N 3:597–607.
[3] Razin S. V., Hancock R., Iarovaia O., Westergaard O., Gromova I., Georgiev G. P. Structural-functional organization of chromosomal DNA domains Cold Spring Harbour Symp. Quant. Biol 1993 58:25–35.
[4] Razin S. V. The nuclear matrix and spatial organization of chromosomal DNA domains. Austin, 1997; 195 p.
[5] Vassetzky Y. S., Hair A., Razin S. V. Rearrangement of chromatin domains in cancer and development J. Cell Biochem 2000 S35, suppl:54–60.
[6] Cockerill P. N., Garrard W. T. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites Cell 1986 44, N 2:273–282.
[7] Mirkovitch J., Mirault M. E., Laemmli U. K. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold Cell 1984 39, N 1:223–232.
[8] Bode J., Stengert-Iber M., Kay V., Schlake T., Dietz-Pfeilstetter A. Scaffold/matrix-attached regions: topological switches with multiple regulatory functions Crit. Rev. Eukaryot. Gene Exp 1996 6, N 2–3:115–138.
[9] Iarovaia O., Hancock R., Lagarkova M., Miassod R., Razin S. V. Mapping of genomic DNA loop organization in a 500-kilobase region of the Drosophila X chromosome by the topoisomerase II-mediated DNA loop excision protocol. Mol. Cell. Biol. 1996; 16(1):302–308.
[10] Hempel K., Stratling W. H. The chicken lysozyme gene 5'MAR and the Drosophila histone SAR are electroelutable from encapsulated and digested nuclei. J. Cell. Sci. 1996; 109(pt 6):1459–1469.
[11] Amati B., Pick L., Laroche T., Gasser S. M. Nuclear scaffold attachment stimulates, but is not essential for ARS activity in Saccharomyces cerevisiae: analysis of the Drosophila ftz SAR EMBO J 1990 9, N 2:4007–4016.
[12] Baiker A., Maercker C., Piechaczek C., Schmidt S. B., Bode J., Benham C., Lipps H. J. Mitotic stability of an episomal vector containing a human scaffold/matrix-attached region is provided by association with nuclear matrix Nat. Cell Biol 2000 2, N 3:182–184.
[13] Webb C., Zong R. T., Lin D., Wang Z., Kaplan M., Paulin Y., Smith E., Probst L., Bryant J., Goldstein A., Scheuermann R., Tucker P. Differential regulation of immunoglobulin gene transcription via nuclear matrix-associated regions Cold Spring Harbour Symp. Quant. Biol 1999 64:109–118.
[14] Harraghy N., Gaussin A., Mermod N. Sustained transgene expressionf using MAR elements Curr. Gene Ther 2008 8, N 5:353–366.
[15] Cockerill P. N., Garrard W. T. Chromosomal loop anchorage sites appear to be evolutionarily conserved FEBS Lett 1986 204, N 1:5–7.
[16] Bogdanova A. N., Razin S. V., Vassetzky Y. S. Nuclear matrixassociated DNA fragments enhance autonomous replication of plasmids in chicken cells Biochimie 1995 77, N 11 P. 880–887.
[17] Vassetzky Y. S., Bogdanova A. N., Razin S. V. Analysis of the chicken DNA fragments that contain structural sites of attachment to the nuclear matrix: DNA-matrix interactions and replication J. Cell Biochem 2000 79, N 1:1–14.
[18] Beug H., von Kirchbach A., Doderlein G., Conscience J. F., Graf T. Chicken hematopoietic cells transformed by seven strains of defective avian leukemia viruses display three distinct phenotypes of differentiation Cell 1979 18, N 3 P. 375–390.
[19] Gasser S. M., Vassetzky Y. S. Analysis of nuclear scaffold attachment regions, in chromatin: a practical approach. Ed. H. Gould Oxford: Oxford Univ. press, 1998:111–124.
[20] Razin S. V., Kekelidze M. G., Lukanidin E. M., Scherrer K., Georgiev G. P. Replication origins are attached to the nuclear skeleton Nucl. Acids Res 1986 14, N 20:8189–8207.
[21] Klehr D., Maass K., Bode J. Scaffold-attached regions from the human IFN-beta domain can be used to enhance the stable expression of genes under the control of various promoters Biochemistry 1991 30, N 5:1264–1270.
[22] Cook P. R. The organization of replication and transcription Science 1999 284, N 5421:1790–1795.
[23] Linnemann A. K., Krawetz S. A. Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity Nucl. Acids Res 2009 37, N 9:2779–2788.
[24] Vassetzky Y., Hair A., Mechali M. Rearrangement of chromatin domains during development in Xenopus Genes Develop 2000 14, N 12:1541–1552.
[25] Eivazova E. R., Gavrilov A., Pirozhkova I., Petrov A., Iarovaia O. V., Razin S. V., Lipinski M., Vassetzky Y. S. Interaction in vivo between the two matrix attachment regions flanking a single chromatin loop J. Mol. Biol 2009 386, N 4 :929–937.
[26] Von Kries J., Buhrmester H., Stratling W. H. A matrix/scaffold attachment region binding protein: identification, purification, and mode of binding Cell 1991 64, N 1:123–135.
[27] Von Kries J. P., Buck F., Stratling W. H. Chicken MAR binding protein P120 is identical to human heterogeneous nuclear ribonucleoprotein (hnRNP) U Nucl. Acids Res 1994 22, N 7:1215–1220.
[28] Han H. J., Russo J., Kohwi Y., Kohwi-Shigematsu T. SATB1 reprogrammes gene expression to promote breast tumour growth and metastasis Nature 2008 452, N 7184:187–193.
[29] Britanova O., Akopov S., Lukyanov S., Gruss P., Tarabykin V. Novel transcription factor Satb2 interacts with matrix attachment region DNA elements in a tissue-specific manner and demonstrates cell-type-dependent expression in the developing mouse CNS Eur. J. Neurosci 2005 21, N 3 P. 658–668.