Abstract
The fate of parental nucleosomes during chromatin replication was studied in vitro using in vitro assembled chromatin containing the whole SV40 genome as well as salt-treated and native SV40 minichromosomes. In vitro assembled minichromosomes were able to replicate efficiently in vitro, when the DNA was preincubated with T-antigen, a cytosolic S100 extract and three deoxynucleoside triphosphates prior to chromatin assembly, indicating that the origin has to be free of nucleosomes for replication initiation. The chromatin structure of the newly synthesized daughter strands in replicating molecules was analysed by psoralen cross-linking of the DNA and by micrococcal nuclease digestion. A 5- and 10-fold excess of protein-free competitor DNA present during minichromosome replication traps the segregating histones. In opposition to published data this suggests that the parental histones remain only loosely or not attached to the DNA in the region of the replication fork. Replication in the putative absence of free histones shows that a subnucleosomal particle is randomly assembled on the daughter strands. The data are compatible with the formation of a H3/H4 tetramer complex under these conditions, supporting the notion that under physiological conditions nucleosome core assembly on the newly synthesized daughter strands occurs by the binding of H2A/H2B dimers to a H3/H4 tetramer complex.
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- Bonne-Andrea C., Wong M. L., Alberts B. M. In vitro replication through nucleosomes without histone displacement. Nature. 1990 Feb 22;343(6260):719–726. doi: 10.1038/343719a0. [DOI] [PubMed] [Google Scholar]
- Boyer H. W., Roulland-Dussoix D. A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol. 1969 May 14;41(3):459–472. doi: 10.1016/0022-2836(69)90288-5. [DOI] [PubMed] [Google Scholar]
- Cech T. R., Potter D., Pardue M. L. Chromatin structure in living cells. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 1):191–198. doi: 10.1101/sqb.1978.042.01.021. [DOI] [PubMed] [Google Scholar]
- Cheng L. Z., Workman J. L., Kingston R. E., Kelly T. J. Regulation of DNA replication in vitro by the transcriptional activation domain of GAL4-VP16. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):589–593. doi: 10.1073/pnas.89.2.589. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng L., Kelly T. J. Transcriptional activator nuclear factor I stimulates the replication of SV40 minichromosomes in vivo and in vitro. Cell. 1989 Nov 3;59(3):541–551. doi: 10.1016/0092-8674(89)90037-8. [DOI] [PubMed] [Google Scholar]
- Clark D. J., Felsenfeld G. A nucleosome core is transferred out of the path of a transcribing polymerase. Cell. 1992 Oct 2;71(1):11–22. doi: 10.1016/0092-8674(92)90262-b. [DOI] [PubMed] [Google Scholar]
- Conconi A., Losa R., Koller T., Sogo J. M. Psoralen-crosslinking of soluble and of H1-depleted soluble rat liver chromatin. J Mol Biol. 1984 Oct 5;178(4):920–928. doi: 10.1016/0022-2836(84)90319-x. [DOI] [PubMed] [Google Scholar]
- Conconi A., Widmer R. M., Koller T., Sogo J. M. Two different chromatin structures coexist in ribosomal RNA genes throughout the cell cycle. Cell. 1989 Jun 2;57(5):753–761. doi: 10.1016/0092-8674(89)90790-3. [DOI] [PubMed] [Google Scholar]
- Cusick M. E., DePamphilis M. L., Wassarman P. M. Dispersive segregation of nucleosomes during replication of simian virus 40 chromosomes. J Mol Biol. 1984 Sep 15;178(2):249–271. doi: 10.1016/0022-2836(84)90143-8. [DOI] [PubMed] [Google Scholar]
- Fotedar R., Roberts J. M. Multistep pathway for replication-dependent nucleosome assembly. Proc Natl Acad Sci U S A. 1989 Sep;86(17):6459–6463. doi: 10.1073/pnas.86.17.6459. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Glikin G. C., Ruberti I., Worcel A. Chromatin assembly in Xenopus oocytes: in vitro studies. Cell. 1984 May;37(1):33–41. doi: 10.1016/0092-8674(84)90298-8. [DOI] [PubMed] [Google Scholar]
- Gruss C., Gutierrez C., Burhans W. C., DePamphilis M. L., Koller T., Sogo J. M. Nucleosome assembly in mammalian cell extracts before and after DNA replication. EMBO J. 1990 Sep;9(9):2911–2922. doi: 10.1002/j.1460-2075.1990.tb07482.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gruss C., Sogo J. M. Chromatin replication. Bioessays. 1992 Jan;14(1):1–8. doi: 10.1002/bies.950140102. [DOI] [PubMed] [Google Scholar]
- Guo Z. S., DePamphilis M. L. Specific transcription factors stimulate simian virus 40 and polyomavirus origins of DNA replication. Mol Cell Biol. 1992 Jun;12(6):2514–2524. doi: 10.1128/mcb.12.6.2514. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guo Z. S., Gutierrez C., Heine U., Sogo J. M., Depamphilis M. L. Origin auxiliary sequences can facilitate initiation of simian virus 40 DNA replication in vitro as they do in vivo. Mol Cell Biol. 1989 Sep;9(9):3593–3602. doi: 10.1128/mcb.9.9.3593. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hanson C. V., Shen C. K., Hearst J. E. Cross-linking of DNA in situ as a probe for chromatin structure. Science. 1976 Jul 2;193(4247):62–64. doi: 10.1126/science.935855. [DOI] [PubMed] [Google Scholar]
- Hoang A. T., Wang W., Gralla J. D. The replication activation potential of selected RNA polymerase II promoter elements at the simian virus 40 origin. Mol Cell Biol. 1992 Jul;12(7):3087–3093. doi: 10.1128/mcb.12.7.3087. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ishimi Y. Preincubation of T antigen with DNA overcomes repression of SV40 DNA replication by nucleosome assembly. J Biol Chem. 1992 May 25;267(15):10910–10913. [PubMed] [Google Scholar]
- Jackson V. Deposition of newly synthesized histones: misinterpretations due to cross-linking density-labeled proteins with Lomant's reagent. Biochemistry. 1987 Apr 21;26(8):2325–2334. doi: 10.1021/bi00382a038. [DOI] [PubMed] [Google Scholar]
- Jackson V. In vivo studies on the dynamics of histone-DNA interaction: evidence for nucleosome dissolution during replication and transcription and a low level of dissolution independent of both. Biochemistry. 1990 Jan 23;29(3):719–731. doi: 10.1021/bi00455a019. [DOI] [PubMed] [Google Scholar]
- Jakobovits E. B., Bratosin S., Aloni Y. A nucleosome-free region in SV40 minichromosomes. Nature. 1980 May 22;285(5762):263–265. doi: 10.1038/285263a0. [DOI] [PubMed] [Google Scholar]
- Klempnauer K. H., Fanning E., Otto B., Knippers R. Maturation of newly replicated chromatin of simian virus 40 and its host cell. J Mol Biol. 1980 Feb 5;136(4):359–374. doi: 10.1016/0022-2836(80)90395-2. [DOI] [PubMed] [Google Scholar]
- Koller T., Kübler O., Portmann R., Sogo J. M. High resolution physical mapping of specific binding sites of Escherichia coli RNA polymerase on the DNA of bacteriophage T7 . J Mol Biol. 1978 Mar 25;120(1):121–131. doi: 10.1016/0022-2836(78)90298-x. [DOI] [PubMed] [Google Scholar]
- Krude T., Knippers R. Transfer of nucleosomes from parental to replicated chromatin. Mol Cell Biol. 1991 Dec;11(12):6257–6267. doi: 10.1128/mcb.11.12.6257. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Krude T., de Maddalena C., Knippers R. A nucleosome assembly factor is a constituent of simian virus 40 minichromosomes. Mol Cell Biol. 1993 Feb;13(2):1059–1068. doi: 10.1128/mcb.13.2.1059. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lanford R. E. Expression of simian virus 40 T antigen in insect cells using a baculovirus expression vector. Virology. 1988 Nov;167(1):72–81. doi: 10.1016/0042-6822(88)90055-4. [DOI] [PubMed] [Google Scholar]
- Li J. J., Kelly T. J. Simian virus 40 DNA replication in vitro. Proc Natl Acad Sci U S A. 1984 Nov;81(22):6973–6977. doi: 10.1073/pnas.81.22.6973. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lusky M., Botchan M. Inhibition of SV40 replication in simian cells by specific pBR322 DNA sequences. Nature. 1981 Sep 3;293(5827):79–81. doi: 10.1038/293079a0. [DOI] [PubMed] [Google Scholar]
- Peden K. W., Pipas J. M., Pearson-White S., Nathans D. Isolation of mutants of an animal virus in bacteria. Science. 1980 Sep 19;209(4463):1392–1396. doi: 10.1126/science.6251547. [DOI] [PubMed] [Google Scholar]
- Randall S. K., Kelly T. J. The fate of parental nucleosomes during SV40 DNA replication. J Biol Chem. 1992 Jul 15;267(20):14259–14265. [PubMed] [Google Scholar]
- Rodríguez-Campos A., Shimamura A., Worcel A. Assembly and properties of chromatin containing histone H1. J Mol Biol. 1989 Sep 5;209(1):135–150. doi: 10.1016/0022-2836(89)90177-0. [DOI] [PubMed] [Google Scholar]
- Sapp M., Worcel A. Purification and mechanism of action of a nucleosome assembly factor from Xenopus oocytes. J Biol Chem. 1990 Jun 5;265(16):9357–9365. [PubMed] [Google Scholar]
- Saragosti S., Moyne G., Yaniv M. Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA. Cell. 1980 May;20(1):65–73. doi: 10.1016/0092-8674(80)90235-4. [DOI] [PubMed] [Google Scholar]
- Shimamura A., Tremethick D., Worcel A. Characterization of the repressed 5S DNA minichromosomes assembled in vitro with a high-speed supernatant of Xenopus laevis oocytes. Mol Cell Biol. 1988 Oct;8(10):4257–4269. doi: 10.1128/mcb.8.10.4257. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shimamura A., Worcel A. The assembly of regularly spaced nucleosomes in the Xenopus oocyte S-150 extract is accompanied by deacetylation of histone H4. J Biol Chem. 1989 Aug 25;264(24):14524–14530. [PubMed] [Google Scholar]
- Simanis V., Lane D. P. An immunoaffinity purification procedure for SV40 large T antigen. Virology. 1985 Jul 15;144(1):88–100. doi: 10.1016/0042-6822(85)90308-3. [DOI] [PubMed] [Google Scholar]
- Smith S., Stillman B. Stepwise assembly of chromatin during DNA replication in vitro. EMBO J. 1991 Apr;10(4):971–980. doi: 10.1002/j.1460-2075.1991.tb08031.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sogo J. M., Ness P. J., Widmer R. M., Parish R. W., Koller T. Psoralen-crosslinking of DNA as a probe for the structure of active nucleolar chromatin. J Mol Biol. 1984 Oct 5;178(4):897–919. doi: 10.1016/0022-2836(84)90318-8. [DOI] [PubMed] [Google Scholar]
- Sogo J. M., Stahl H., Koller T., Knippers R. Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures. J Mol Biol. 1986 May 5;189(1):189–204. doi: 10.1016/0022-2836(86)90390-6. [DOI] [PubMed] [Google Scholar]
- Sogo J. M., Thoma F. Electron microscopy of chromatin. Methods Enzymol. 1989;170:142–165. doi: 10.1016/0076-6879(89)70045-8. [DOI] [PubMed] [Google Scholar]
- Stillman B. W., Gluzman Y. Replication and supercoiling of simian virus 40 DNA in cell extracts from human cells. Mol Cell Biol. 1985 Aug;5(8):2051–2060. doi: 10.1128/mcb.5.8.2051. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sugasawa K., Ishimi Y., Eki T., Hurwitz J., Kikuchi A., Hanaoka F. Nonconservative segregation of parental nucleosomes during simian virus 40 chromosome replication in vitro. Proc Natl Acad Sci U S A. 1992 Feb 1;89(3):1055–1059. doi: 10.1073/pnas.89.3.1055. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wolffe A. P. Implications of DNA replication for eukaryotic gene expression. J Cell Sci. 1991 Jun;99(Pt 2):201–206. doi: 10.1242/jcs.99.2.201. [DOI] [PubMed] [Google Scholar]
- Worcel A., Han S., Wong M. L. Assembly of newly replicated chromatin. Cell. 1978 Nov;15(3):969–977. doi: 10.1016/0092-8674(78)90280-5. [DOI] [PubMed] [Google Scholar]
- Yang L., Wold M. S., Li J. J., Kelly T. J., Liu L. F. Roles of DNA topoisomerases in simian virus 40 DNA replication in vitro. Proc Natl Acad Sci U S A. 1987 Feb;84(4):950–954. doi: 10.1073/pnas.84.4.950. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zucker K., Worcel A. The histone H3/H4.N1 complex supplemented with histone H2A-H2B dimers and DNA topoisomerase I forms nucleosomes on circular DNA under physiological conditions. J Biol Chem. 1990 Aug 25;265(24):14487–14496. [PubMed] [Google Scholar]