Determination of the in vivo distribution of nuclear matrix attachment regions using a polymerase chain reaction-based assay in Arabidopsis thaliana

Journal of Bioscience and Bioengineering

Volumn 108, Issue 1, 2009, Pages 11-19

  Tachiki, Kensuke ^a   Kodama, Yuichi ^b   Nakayama, Hideki ^a   Shinmyo, Atsuhiko ^a  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Arabidopsis thaliana; Chromatin loop; DNase I hypersensitive site; In vitro MAR binding assay; In vivo MAR PCR assay; Matrix attachment region; Nuclear matrix

Indexed keywords

ARABIDOPSIS THALIANA; CHROMATIN LOOP; DNASE I HYPERSENSITIVE SITE; IN VITRO MAR BINDING ASSAY; IN VIVO MAR-PCR ASSAY; MATRIX ATTACHMENT REGION; NUCLEAR MATRIX;

ANIMALS; GENES; NUCLEIC ACIDS; PATIENT MONITORING; POLYMERIZATION; TOBACCO;

BINDING SITES;

DEOXYRIBONUCLEASE I;

ARABIDOPSIS; ARTICLE; CHROMATIN; DNA FLANKING REGION; EUKARYOTE; IN VIVO STUDY; MATRIX ATTACHMENT REGION; REAL TIME POLYMERASE CHAIN REACTION;

ARABIDOPSIS; BASE SEQUENCE; DNA PRIMERS; GENOME, PLANT; MATRIX ATTACHMENT REGIONS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

ANIMALIA; ARABIDOPSIS THALIANA; EUKARYOTA;

EID: 67649410722     PISSN: 13891723     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiosc.2009.02.010     Document Type: Article

References (37)

1. Shaposhnikov S.A., Akopov S.B., Chernov I.P., Thomsen P.D., Joergensen C., Collins A.R., Frengen E., and Nikolaev L.G. A map of nuclear matrix attachment regions within the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1. Genomics 89 (2007) 354-361
2. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389 (1997) 251-260
3. Jackson D.A., Yuan J., and Cook P.R. A gentle method for preparing cyto- and nucleo-skeletons and associated chromatin. J. Cell. Sci. 90 (1988) 365-378
4. Amati B.B., and Gasser S.M. Chromosomal ARS and CEN elements bind specifically to the yeast nuclear scaffold. Cell 54 (1988) 967-978
5. Mirkovitch J., Mirault M.E., and Laemmli U.K. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39 (1984) 223-232
6. Cockerill P.N., and Garrard W.T. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44 (1986) 273-282
7. Hall G., Allen G.C., Loer D.S., Thompson W.F., and Spiker S. Nuclear scaffolds and scaffold-attachment regions in higher plants. Proc. Natl. Acad. Sci. U. S. A. 88 (1991) 9320-9324
8. Avramova Z., Tikhonov A., Chen M., and Bennetzen J.L. Matrix attachment regions and structural colinearity in the genomes of two grass species. Nucleic Acids Res. 26 (1998) 761-767
9. Heng H.H., Goetze S., Ye C.J., Liu G., Stevens J.B., Bremer S.W., Wykes S.M., Bode J., and Krawetz S.A. Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J. Cell. Sci. 117 (2004) 999-1008
10. Boulikas T. Nature of DNA sequences at the attachment regions of genes to the nuclear matrix. J. Cell. Biochem. 52 (1993) 14-22
11. Bode J., Kohwi Y., Dickinson L., Joh T., Klehr D., Mielke C., and Kohwi-Shigematsu T. Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255 (1992) 195-197
12. Yamasaki K., Akiba T., Yamasaki T., and Harata K. Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1. Nucleic Acids Res. 35 (2007) 5073-5084
13. Martins R.P., and Krawetz S.A. Decondensing the protamine domain for transcription. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 8340-8345
14. Sabo P.J., Hawrylycz M., Wallace J.C., Humbert R., Yu M., Shafer A., Kawamoto J., Hall R., Mack J., Dorschner M.O., McArthur M., and Stamatoyannopoulos J.A. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 16837-16842
15. Jackson D.A., Dickinson P., and Cook P.R. The size of chromatin loops in HeLa cells. EMBO J. 9 (1990) 567-571
16. Chernov I.P., Akopov S.B., and Nikolaev L.G. Structure and functions of nuclear matrix associated regions (S/MARs). Russ. J. Bioorg. Chem. 30 (2004) 1-11
17. van Drunen C.M., Oosterling R.W., Keultjes G.M., Weisbeek P.J., van Driel R., and Smeekens S.C. Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana. Nucleic Acids Res. 25 (1997) 3904-3911
18. Rudd S., Frisch M., Grote K., Meyers B.C., Mayer K., and Werner T. Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiol. 135 (2004) 715-722
19. Axelos M., Curie C., Mazzolini L., Bardet C., and Lescure B. A protocol for transient gene expression in Arabidopsis thaliana protoplasts isolated from cell suspension cultures. Plant Physiol. Biochem. 30 (1992) 123-128
20. Kodama Y., Nagaya S., Shinmyo A., and Kato K. Mapping and characterization of DNase I hypersensitive sites in Arabidopsis chromatin. Plant Cell Physiol. 48 (2007) 459-470
21. Satoh J., Kato K., and Shinmyo A. The 5′-untranslated region of the tobacco alcohol dehydrogenase gene functions as an effective translational enhancer in plant. J. Biosci. Bioeng. 98 (2004) 1-8
22. Hall G.E., and Spiker S. Isolation and characterization of nuclear scaffolds, p 1-12. In: Gelvin S., Schilperoort R., and Verma D.P. (Eds). Plant molecular biology manual, Vol. D2 (1994), Kluwer, Dordrecht
23. Toyoda T., and Shinozaki K. Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models. Plant J. 43 (2005) 611-621
24. Sawasaki T., Takahashi M., Goshima N., and Morikawa H. Structures of transgene loci in transgenic Arabidopsis plants obtained by particle bombardment: junction regions can bind to nuclear matrices. Gene 218 (1998) 27-35
25. The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (2000) 796-815
26. Singh G.B., Kramer J.A., and Krawetz S.A. Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Res. 25 (1997) 1419-1425
27. Kieffer L.J., Greally J.M., Landres I., Nag S., Nakajima Y., Kohwi-Shigematsu T., and Kavathas P.B. Identification of a candidate regulatory region in the human CD8 gene complex by colocalization of DNase I hypersensitive sites and matrix attachment regions which bind SATB1 and GATA-3. J. Immunol. 168 (2002) 3915-3922
28. Mauldin S.K., Getts R.C., Liu W., and Stamato T.D. DNA-PK-dependent binding of DNA ends to plasmids containing nuclear matrix attachment region DNA sequences: evidence for assembly of a repair complex. Nucleic Acids Res. 30 (2002) 4075-4087
29. Paul A.L., and Ferl R.J. Higher order chromatin structures in maize and Arabidopsis. Plant Cell 10 (1998) 1349-1359
30. Paul A.L., and Ferl R.J. Higher-order chromatin structure: looping long molecules. Plant Mol. Biol. 41 (1999) 713-720
31. Morisawa G., Han-Yama A., Moda I., Tamai A., Iwabuchi M., and Meshi T. AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region. Plant Cell 12 (2000) 1903-1916
32. Kumar P.P., Bischof O., Purbey P.K., Notani D., Urlaub H., Dejean A., and Galande S. Functional interaction between PML and SATB1 regulates chromatin-loop architecture and transcription of the MHC class I locus. Nat. Cell Biol. 9 (2007) 45-56
33. Murphy W.J., Larkin D.M., Everts-van der Wind A., Bourque G., Tesler G., Auvil L., Beever J.E., Chowdhary B.P., Galibert F., and Gatzke L. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309 (2005) 613-617
34. Song R., Llaca V., and Messing J. Mosaic organization of orthologous sequences in grass genomes. Genome Res. 12 (2002) 1549-1555
35. Halweg C., Thompson W.F., and Spiker S. The rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: a flow cytometric study. Plant Cell 17 (2005) 418-429
36. Petrov A., Allinne J., Pirozhkova I., Laoudj D., Lipinski M., and Vassetzky Y.S. A nuclear matrix attachment site in the 4q35 locus has an enhancer-blocking activity in vivo: implications for the facio-scapulo-humeral dystrophy. Genome Res. 18 (2008) 39-45
37. Donev R.M. The type of DNA attachment sites recovered from nuclear matrix depends on isolation procedure used. Mol. Cell. Biochem. 214 (2000) 103-110