Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1996 Apr 1;24(7):1330–1336. doi: 10.1093/nar/24.7.1330

Construction of a chromosome specific library of human MARs and mapping of matrix attachment regions on human chromosome 19.

L G Nikolaev 1, T Tsevegiyn 1, S B Akopov 1, L K Ashworth 1, E D Sverdlov 1
PMCID: PMC145782  PMID: 8614638

Abstract

Using a novel procedure a representative human chromosome 19-specific library was constructed of short sequences, which bind preferentially to the nuclear matrix (matrix attachment regions, or MARs). Judging by 20 clones sequenced so far, the library contains > 50% of human inserts, about 90% of which are matrix-binding by the in vitro test. Computer analysis of sequences of eight human MARs did not reveal any significant homologies with the EMBL Nucleotide Data Base entries as well as between MARs themselves. Eight MARs were assigned to individual positions on the chromosome 19 physical map. The library constructed can serve as a good source of MAR sequences for comparative analysis and classification and for further chromosome mapping of MARs as well.

Full Text

The Full Text of this article is available as a PDF (112.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams M. D., Kelley J. M., Gocayne J. D., Dubnick M., Polymeropoulos M. H., Xiao H., Merril C. R., Wu A., Olde B., Moreno R. F. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991 Jun 21;252(5013):1651–1656. doi: 10.1126/science.2047873. [DOI] [PubMed] [Google Scholar]
  2. Adams M. D., Kerlavage A. R., Fields C., Venter J. C. 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nat Genet. 1993 Jul;4(3):256–267. doi: 10.1038/ng0793-256. [DOI] [PubMed] [Google Scholar]
  3. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  4. Ashworth L. K., Batzer M. A., Brandriff B., Branscomb E., de Jong P., Garcia E., Garnes J. A., Gordon L. A., Lamerdin J. E., Lennon G. An integrated metric physical map of human chromosome 19. Nat Genet. 1995 Dec;11(4):422–427. doi: 10.1038/ng1295-422. [DOI] [PubMed] [Google Scholar]
  5. Billings P. R., Smith C. L., Cantor C. R. New techniques for physical mapping of the human genome. FASEB J. 1991 Jan;5(1):28–34. doi: 10.1096/fasebj.5.1.1846833. [DOI] [PubMed] [Google Scholar]
  6. Bode J., Kohwi Y., Dickinson L., Joh T., Klehr D., Mielke C., Kohwi-Shigematsu T. Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science. 1992 Jan 10;255(5041):195–197. doi: 10.1126/science.1553545. [DOI] [PubMed] [Google Scholar]
  7. Borodin A., Kopatnzev E., Wagner L., Volik S., Ermolaeva O., Lebedev Y., Monastyrskaya G., Kunz J., Grzeschik K. H., Sverdlov E. An arrayed library enriched in hncDNA corresponding to transcribed sequences of human chromosome 19: preparation and analysis. Genet Anal. 1995 Mar;12(1):23–31. doi: 10.1016/1050-3862(95)00106-9. [DOI] [PubMed] [Google Scholar]
  8. Boulikas T., Kong C. F. Multitude of inverted repeats characterizes a class of anchorage sites of chromatin loops to the nuclear matrix. J Cell Biochem. 1993 Sep;53(1):1–12. doi: 10.1002/jcb.240530802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Boulikas T. Nature of DNA sequences at the attachment regions of genes to the nuclear matrix. J Cell Biochem. 1993 May;52(1):14–22. doi: 10.1002/jcb.240520104. [DOI] [PubMed] [Google Scholar]
  10. Brandriff B., Gordon L., Trask B. A new system for high-resolution DNA sequence mapping interphase pronuclei. Genomics. 1991 May;10(1):75–82. doi: 10.1016/0888-7543(91)90486-x. [DOI] [PubMed] [Google Scholar]
  11. Carrano A. V., de Jong P. J., Branscomb E., Slezak T., Watkins B. W. Constructing chromosome- and region-specific cosmid maps of the human genome. Genome. 1989;31(2):1059–1065. doi: 10.1139/g89-182. [DOI] [PubMed] [Google Scholar]
  12. 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 Jan 31;44(2):273–282. doi: 10.1016/0092-8674(86)90761-0. [DOI] [PubMed] [Google Scholar]
  13. Collins F., Galas D. A new five-year plan for the U.S. Human Genome Project. Science. 1993 Oct 1;262(5130):43–46. doi: 10.1126/science.8211127. [DOI] [PubMed] [Google Scholar]
  14. Getzenberg R. H., Pienta K. J., Coffey D. S. The tissue matrix: cell dynamics and hormone action. Endocr Rev. 1990 Aug;11(3):399–417. doi: 10.1210/edrv-11-3-399. [DOI] [PubMed] [Google Scholar]
  15. Hochgeschwender U. Toward a transcriptional map of the human genome. Trends Genet. 1992 Feb;8(2):41–44. doi: 10.1016/0168-9525(92)90336-3. [DOI] [PubMed] [Google Scholar]
  16. Izaurralde E., Mirkovitch J., Laemmli U. K. Interaction of DNA with nuclear scaffolds in vitro. J Mol Biol. 1988 Mar 5;200(1):111–125. doi: 10.1016/0022-2836(88)90337-3. [DOI] [PubMed] [Google Scholar]
  17. Jackson D. A., Dolle A., Robertson G., Cook P. R. The attachments of chromatin loops to the nucleoskeleton. Cell Biol Int Rep. 1992 Aug;16(8):687–696. doi: 10.1016/s0309-1651(05)80013-x. [DOI] [PubMed] [Google Scholar]
  18. McKusick V. A. Current trends in mapping human genes. FASEB J. 1991 Jan;5(1):12–20. doi: 10.1096/fasebj.5.1.1991580. [DOI] [PubMed] [Google Scholar]
  19. Mirkovitch J., Mirault M. E., Laemmli U. K. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell. 1984 Nov;39(1):223–232. doi: 10.1016/0092-8674(84)90208-3. [DOI] [PubMed] [Google Scholar]
  20. Obradovich D., Borodin A. M., Kopantsev E. P., Vagner L. L., Volik S. V., Ermolaeva O. D., Lebedev Iu B., Monastyrskaia G. S., Sverdlov E. D. Poluchenie i kharakteristiki uporiadochennoi biblioteki transkribiruemykh posledovatel'nostei khromosomy 19 cheloveka iz gibridnykh kletok chelovek-khomiak. Bioorg Khim. 1994 Aug-Sep;20(8-9):919–931. [PubMed] [Google Scholar]
  21. Polymeropoulos M. H., Xiao H., Glodek A., Gorski M., Adams M. D., Moreno R. F., Fitzgerald M. G., Venter J. C., Merril C. R. Chromosomal assignment of 46 brain cDNAs. Genomics. 1992 Mar;12(3):492–496. doi: 10.1016/0888-7543(92)90439-y. [DOI] [PubMed] [Google Scholar]
  22. Polymeropoulos M. H., Xiao H., Sikela J. M., Adams M., Venter J. C., Merril C. R. Chromosomal distribution of 320 genes from a brain cDNA library. Nat Genet. 1993 Aug;4(4):381–386. doi: 10.1038/ng0893-381. [DOI] [PubMed] [Google Scholar]
  23. Stephens J. C., Cavanaugh M. L., Gradie M. I., Mador M. L., Kidd K. K. Mapping the human genome: current status. Science. 1990 Oct 12;250(4978):237–244. doi: 10.1126/science.2218527. [DOI] [PubMed] [Google Scholar]
  24. Vemuri M. C., Raju N. N., Malhotra S. K. Recent advances in nuclear matrix function. Cytobios. 1993;76(305):117–128. [PubMed] [Google Scholar]
  25. Volik S., Lebedev Y., Nikolaev L., Shevchenko Y., Vinogradova T., Kopantzev E., Kolesnik T., Monastyrskaya G., Kunz U., Grzeschik K. H. Mapping of transcribed sequences on human chromosome 19. DNA Seq. 1995;6(1):13–26. doi: 10.3109/10425179509074694. [DOI] [PubMed] [Google Scholar]
  26. Weissenbach J., Gyapay G., Dib C., Vignal A., Morissette J., Millasseau P., Vaysseix G., Lathrop M. A second-generation linkage map of the human genome. Nature. 1992 Oct 29;359(6398):794–801. doi: 10.1038/359794a0. [DOI] [PubMed] [Google Scholar]
  27. Zlatanova J. S., van Holde K. E. Chromatin loops and transcriptional regulation. Crit Rev Eukaryot Gene Expr. 1992;2(3):211–224. [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES