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. 1981 Jan 24;9(2):349–363. doi: 10.1093/nar/9.2.349

Association of newly replicated DNA with the nuclear matrix of Physarum polycephalum.

B F Hunt, B Vogelstein
PMCID: PMC326697  PMID: 7208354

Abstract

We have studied the role of the nuclear matrix in DNA replication in a naturally synchronized eucaryote, Physarum polycephalum. When P. polycephalum. When P. polycephalum macroplasmodia were pulse labeled with 3H-thymidine, the DNA remaining tightly associated with the matrix was highly enriched in newly synthesized DNA. This enrichment was found both in nuclei that had just initiated DNA replication as well as in nuclei isolated later during S phase. Pulse chase experiments showed that the association of newly replicated DNA with the matrix is transient, since most of the newly replicated DNA could be chased from the matrix by incubating pulse labeled macroplasmodia in media containing unlabeled thymidine. Studies measuring the size distribution of the matrix DNA supported the hypothesis that replication forks are attached to the nuclear matrix. Reconstitution controls indicated that these results were unlikely to be due to preferential, nonspecific binding of nascent DNA to the matrix during the extraction procedures. These results with P. polycephalum in combination with previous studies in non-synchronized rodent cells, suggest that the association of newly replicated DNA with the nuclear matrix may be a general feature of eucaryotic DNA replication.

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Selected References

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

  1. Aaronson R. P., Blobel G. Isolation of nuclear pore complexes in association with a lamina. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1007–1011. doi: 10.1073/pnas.72.3.1007. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Benyajati C., Worcel A. Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. Cell. 1976 Nov;9(3):393–407. doi: 10.1016/0092-8674(76)90084-2. [DOI] [PubMed] [Google Scholar]
  3. Berezney R., Coffey D. S. Identification of a nuclear protein matrix. Biochem Biophys Res Commun. 1974 Oct 23;60(4):1410–1417. doi: 10.1016/0006-291x(74)90355-6. [DOI] [PubMed] [Google Scholar]
  4. Berezney R., Coffey D. S. Nuclear matrix. Isolation and characterization of a framework structure from rat liver nuclei. J Cell Biol. 1977 Jun;73(3):616–637. doi: 10.1083/jcb.73.3.616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Berezney R., Coffey D. S. Nuclear protein matrix: association with newly synthesized DNA. Science. 1975 Jul 25;189(4199):291–293. doi: 10.1126/science.1145202. [DOI] [PubMed] [Google Scholar]
  6. Braun R., Mittermayer C., Rusch H. P. Sequential temporal replication of DNA in Physarum polycephalum. Proc Natl Acad Sci U S A. 1965 May;53(5):924–931. doi: 10.1073/pnas.53.5.924. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brewer E. N., Evans T. E., Evans H. H. Studies on the mechanism of DNA replication in Physarum polycephalum. J Mol Biol. 1974 Dec 5;90(2):335–342. doi: 10.1016/0022-2836(74)90377-5. [DOI] [PubMed] [Google Scholar]
  8. Cabradilla C. D., Toliver A. P. S-phase dependent forms of DNA - nuclear membrane complexes in HeLa cells. Biochim Biophys Acta. 1975 Aug 21;402(2):188–198. doi: 10.1016/0005-2787(75)90038-6. [DOI] [PubMed] [Google Scholar]
  9. Comings D. E., Kakefuda T. Initiation of deoxyribonucleic acid replication at the nuclear membrane in human cells. J Mol Biol. 1968 Apr 14;33(1):225–229. doi: 10.1016/0022-2836(68)90290-8. [DOI] [PubMed] [Google Scholar]
  10. Cook P. R., Brazell I. A. Supercoils in human DNA. J Cell Sci. 1975 Nov;19(2):261–279. doi: 10.1242/jcs.19.2.261. [DOI] [PubMed] [Google Scholar]
  11. Dijkwel P. A., Mullenders L. H., Wanka F. Analysis of the attachment of replicating DNA to a nuclear matrix in mammalian interphase nuclei. Nucleic Acids Res. 1979 Jan;6(1):219–230. doi: 10.1093/nar/6.1.219. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Erlandson R. A., de Harven E. The ultrastructure of synchronized HeLa cells. J Cell Sci. 1971 Mar;8(2):353–397. doi: 10.1242/jcs.8.2.353. [DOI] [PubMed] [Google Scholar]
  13. Fakan S., Turner G. N., Pagano J. S., Hancock R. Sites of replication of chromosomal DNA in a eukaryotic cell. Proc Natl Acad Sci U S A. 1972 Aug;69(8):2300–2305. doi: 10.1073/pnas.69.8.2300. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fink K., Nygaard P. Purine metabolism in microplasmodia of Physarum polycephalum. Biochim Biophys Acta. 1979 Jul 26;563(2):269–277. doi: 10.1016/0005-2787(79)90046-7. [DOI] [PubMed] [Google Scholar]
  15. Fink K., Nygaard P. Pyrimidine metabolism in microplasmodia of Physarum polycephalum. Eur J Biochem. 1978 Sep 1;89(2):417–424. doi: 10.1111/j.1432-1033.1978.tb12544.x. [DOI] [PubMed] [Google Scholar]
  16. Friedman D. L., Mueller G. C. Studies on the nature of replicating DNA of HeLa cells. Biochim Biophys Acta. 1969 Jan 21;174(1):253–263. doi: 10.1016/0005-2787(69)90249-4. [DOI] [PubMed] [Google Scholar]
  17. Funderud S., Andreassen R., Haugli F. DNA replication in Physarum polycephalum: electron microscopic and autoradiographic analysis of replicating DNA from defined stages of the S-period. Nucleic Acids Res. 1979 Apr;6(4):1417–1431. doi: 10.1093/nar/6.4.1417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Funderud S., Andreassen R., Haugli F. Size distribution and maturation of newly replicated DNA through the S and G2 phases of Physarum polycephalum. Cell. 1978 Dec;15(4):1519–1526. doi: 10.1016/0092-8674(78)90074-0. [DOI] [PubMed] [Google Scholar]
  19. GEORGIEV G. P., CHENTSOV J. S. On the structural organization of nucleolo-chromosomal ribonucleoproteins. Exp Cell Res. 1962 Sep;27:570–572. doi: 10.1016/0014-4827(62)90020-4. [DOI] [PubMed] [Google Scholar]
  20. Gross-Bellard M., Oudet P., Chambon P. Isolation of high-molecular-weight DNA from mammalian cells. Eur J Biochem. 1973 Jul 2;36(1):32–38. doi: 10.1111/j.1432-1033.1973.tb02881.x. [DOI] [PubMed] [Google Scholar]
  21. Hanaoka F., Yamada M. Localization of the replication point of mammalian cell DNA at the membrane. Biochem Biophys Res Commun. 1971 Feb 19;42(4):647–653. doi: 10.1016/0006-291x(71)90537-7. [DOI] [PubMed] [Google Scholar]
  22. Hartwig M. Organization of mammalian chromosomal DNA: supercoiled and folded circular DNA subunits from interphase cell nuclei. Acta Biol Med Ger. 1978;37(3):421–432. [PubMed] [Google Scholar]
  23. Hodge L. D., Mancini P., Davis F. M., Heywood P. Nuclear matrix of HeLa S3 cells. Polypeptide composition during adenovirus infection and in phases of the cell cycle. J Cell Biol. 1977 Jan;72(1):194–208. doi: 10.1083/jcb.72.1.194. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Huberman J. A., Riggs A. D. On the mechanism of DNA replication in mammalian chromosomes. J Mol Biol. 1968 Mar 14;32(2):327–341. doi: 10.1016/0022-2836(68)90013-2. [DOI] [PubMed] [Google Scholar]
  25. Huberman J. A., Tsai A., Deich R. A. DNA replication sites within nuclei of mammalian cells. Nature. 1973 Jan 5;241(5384):32–36. doi: 10.1038/241032a0. [DOI] [PubMed] [Google Scholar]
  26. Ide T., Nakane M., Anzai K., Ando T. Supercoiled DNA folded by non-histone proteins in cultured mammalian cells. Nature. 1975 Dec 4;258(5534):445–447. doi: 10.1038/258445a0. [DOI] [PubMed] [Google Scholar]
  27. Infante A. A., Nauta R., Gilbert S., Hobart P., Firshein W. DNA synthesis in developing sea urchins: role of a DNA-nuclear membrane complex. Nat New Biol. 1973 Mar 7;242(114):5–8. doi: 10.1038/newbio242005a0. [DOI] [PubMed] [Google Scholar]
  28. Long B. H., Huang C. Y., Pogo A. O. Isolation and characterization of the nuclear matrix in Friend erythroleukemia cells: chromatin and hnRNA interactions with the nuclear matrix. Cell. 1979 Dec;18(4):1079–1090. doi: 10.1016/0092-8674(79)90221-6. [DOI] [PubMed] [Google Scholar]
  29. Mitchelson K. R., Bekers A. G., Wanka F. Isolation of a residual protein structure from nuclei of the myxomycete Physarum polycephalum. J Cell Sci. 1979 Oct;39:247–256. doi: 10.1242/jcs.39.1.247. [DOI] [PubMed] [Google Scholar]
  30. Mizuno N. S., Stoops C. E., Sinha A. A. DNA synthesis associated with the inner membrane of the nuclear envelope. Nat New Biol. 1971 Jan 6;229(1):22–24. doi: 10.1038/newbio229022a0. [DOI] [PubMed] [Google Scholar]
  31. Mohberg J., Rusch H. P. Isolation and DNA content of nuclei of Physarum polycephalum. Exp Cell Res. 1971 Jun;66(2):305–316. doi: 10.1016/0014-4827(71)90682-3. [DOI] [PubMed] [Google Scholar]
  32. NYGAARD O. F., GUTTES S., RUSCH H. P. Nucleic acid metabolism in a slime mold with synchronous mitosis. Biochim Biophys Acta. 1960 Feb 26;38:298–306. doi: 10.1016/0006-3002(60)91245-2. [DOI] [PubMed] [Google Scholar]
  33. Narayan K. S., Steele W. J., Smetana K., Busch H. Ultrastructural aspects of the ribonucleo-protein network in nuclei of Walker tumor and rat liver. Exp Cell Res. 1967 Apr;46(1):65–77. doi: 10.1016/0014-4827(67)90409-0. [DOI] [PubMed] [Google Scholar]
  34. Pardoll D. M., Vogelstein B., Coffey D. S. A fixed site of DNA replication in eucaryotic cells. Cell. 1980 Feb;19(2):527–536. doi: 10.1016/0092-8674(80)90527-9. [DOI] [PubMed] [Google Scholar]
  35. Pearson G. D., Hanawalt P. C. Isolation of DNA replication complexes from uninfected and adenovirus-infected HeLa cells. J Mol Biol. 1971 Nov 28;62(1):65–80. doi: 10.1016/0022-2836(71)90131-8. [DOI] [PubMed] [Google Scholar]
  36. Peters K. E., Commings D. E. Two-dimensinal gel electrophoresis of rat liver nuclear washes, nuclear matrix, and hnRNA proteins. J Cell Biol. 1980 Jul;86(1):135–155. doi: 10.1083/jcb.86.1.135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Piñon R., Salts Y. Isolation of folded chromosomes from the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1977 Jul;74(7):2850–2854. doi: 10.1073/pnas.74.7.2850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Prem veer Reddy G., Pardee A. B. Multienzyme complex for metabolic channeling in mammalian DNA replication. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3312–3316. doi: 10.1073/pnas.77.6.3312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. SACHSENMAIER W. ZUR DNS- UND RNS-SYNTHESE IM TEILUNGSCYCLUS SYNCHRONER PLASMODIEN VON PHYSARUM POLYCEPHALUM. Biochem Z. 1964 Nov 6;340:541–547. [PubMed] [Google Scholar]
  40. Smith D. W., Hanawalt P. C. Properties of the growing point region in the bacterial chromosome. Biochim Biophys Acta. 1967 Dec 19;149(2):519–531. doi: 10.1016/0005-2787(67)90180-3. [DOI] [PubMed] [Google Scholar]
  41. Sueoka N., Quinn W. G. Membrane attachment of the chromosome replication origin in Bacillus subtilis. Cold Spring Harb Symp Quant Biol. 1968;33:695–705. doi: 10.1101/sqb.1968.033.01.078. [DOI] [PubMed] [Google Scholar]
  42. Tremblay G. Y., Daniels M. J., Schaechter M. Isolation of a cell membrane-DNA-nascent RNA complex from bacteria. J Mol Biol. 1969 Feb 28;40(1):65–76. doi: 10.1016/0022-2836(69)90296-4. [DOI] [PubMed] [Google Scholar]
  43. Vogelstein B., Pardoll D. M., Coffey D. S. Supercoiled loops and eucaryotic DNA replicaton. Cell. 1980 Nov;22(1 Pt 1):79–85. doi: 10.1016/0092-8674(80)90156-7. [DOI] [PubMed] [Google Scholar]
  44. Williams C. A., Ockey C. H. Distribution of DNA replicator sites in mammalian nuclei after different methods of cell synchronization. Exp Cell Res. 1970 Dec;63(2):365–372. doi: 10.1016/0014-4827(70)90224-7. [DOI] [PubMed] [Google Scholar]
  45. ZBARSKY I. B., DMITRIEVA N. P., YERMOLAYEVA L. P. On the structure of tumor cell nuclei. Exp Cell Res. 1962 Sep;27:573–576. doi: 10.1016/0014-4827(62)90021-6. [DOI] [PubMed] [Google Scholar]
  46. ZBARSKY I. B., GEORGIEV G. P. Cytological characteristics of protein and nucleoprotein fractions of cell nuclei. Biochim Biophys Acta. 1959 Mar;32(1):301–302. doi: 10.1016/0006-3002(59)90600-6. [DOI] [PubMed] [Google Scholar]

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