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Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1985 May;5(5):964–971. doi: 10.1128/mcb.5.5.964

Site-specific DNA binding of nuclear factor I: analyses of cellular binding sites.

R M Gronostajski, S Adhya, K Nagata, R A Guggenheimer, J Hurwitz
PMCID: PMC366811  PMID: 4039788

Abstract

Nuclear factor I is a cellular site-specific DNA-binding protein required for the efficient in vitro replication of adenovirus DNA. We have characterized human DNA sequences to which nuclear factor I binds. Three nuclear factor I binding sites (FIB sites), isolated from HeLa cell DNA, each contain the sequence TGG(N)6-7GCCAA. Comparison with other known and putative FIB sites suggests that this sequence is important for the binding of nuclear factor I. Nuclear factor I protects a 25- to 30-base-pair region surrounding this sequence from digestion by DNase I. Methylation protection studies suggest that nuclear factor I interacts with guanine residues within the TGG(N)6-7GCCAA consensus sequence. One binding site (FIB-2) contained a restriction endonuclease HaeIII cleavage site (GGCC) at the 5' end of the GCCAA motif. Digestion of FIB-2 with HaeIII abolished the binding of nuclear factor I. Southern blot analyses indicate that the cellular FIB sites described here are present within single-copy DNA in the HeLa cell genome.

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Selected References

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  1. Borgmeyer U., Nowock J., Sippel A. E. The TGGCA-binding protein: a eukaryotic nuclear protein recognizing a symmetrical sequence on double-stranded linear DNA. Nucleic Acids Res. 1984 May 25;12(10):4295–4311. doi: 10.1093/nar/12.10.4295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Challberg M. D., Desiderio S. V., Kelly T. J., Jr Adenovirus DNA replication in vitro: characterization of a protein covalently linked to nascent DNA strands. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5105–5109. doi: 10.1073/pnas.77.9.5105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Challberg M. D., Kelly T. J. Eukaryotic DNA replication: viral and plasmid model systems. Annu Rev Biochem. 1982;51:901–934. doi: 10.1146/annurev.bi.51.070182.004345. [DOI] [PubMed] [Google Scholar]
  4. Friefeld B. R., Lichy J. H., Field J., Gronostajski R. M., Guggenheimer R. A., Krevolin M. D., Nagata K., Hurwitz J., Horwitz M. S. The in vitro replication of adenovirus DNA. Curr Top Microbiol Immunol. 1984;110:221–255. doi: 10.1007/978-3-642-46494-2_8. [DOI] [PubMed] [Google Scholar]
  5. Friefeld B. R., Lichy J. H., Hurwitz J., Horwitz M. S. Evidence for an altered adenovirus DNA polymerase in cells infected with the mutant H5ts149. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1589–1593. doi: 10.1073/pnas.80.6.1589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Gronostajski R. M., Field J., Hurwitz J. Purification of a primase activity associated with DNA polymerase alpha from HeLa cells. J Biol Chem. 1984 Aug 10;259(15):9479–9486. [PubMed] [Google Scholar]
  7. Gronostajski R. M., Nagata K., Hurwitz J. Isolation of human DNA sequences that bind to nuclear factor I, a host protein involved in adenovirus DNA replication. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4013–4017. doi: 10.1073/pnas.81.13.4013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Guggenheimer R. A., Stillman B. W., Nagata K., Tamanoi F., Hurwitz J. DNA sequences required for the in vitro replication of adenovirus DNA. Proc Natl Acad Sci U S A. 1984 May;81(10):3069–3073. doi: 10.1073/pnas.81.10.3069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Guo L. H., Wu R. New rapid methods for DNA sequencing based in exonuclease III digestion followed by repair synthesis. Nucleic Acids Res. 1982 Mar 25;10(6):2065–2084. doi: 10.1093/nar/10.6.2065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  11. Lichy J. H., Field J., Horwitz M. S., Hurwitz J. Separation of the adenovirus terminal protein precursor from its associated DNA polymerase: role of both proteins in the initiation of adenovirus DNA replication. Proc Natl Acad Sci U S A. 1982 Sep;79(17):5225–5229. doi: 10.1073/pnas.79.17.5225. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lichy J. H., Horwitz M. S., Hurwitz J. Formation of a covalent complex between the 80,000-dalton adenovirus terminal protein and 5'-dCMP in vitro. Proc Natl Acad Sci U S A. 1981 May;78(5):2678–2682. doi: 10.1073/pnas.78.5.2678. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Lichy J. H., Nagata K., Friefeld B. R., Enomoto T., Field J., Guggenheimer R. A., Ikeda J. E., Horwitz M. S., Hurwitz J. Isolation of proteins involved in the replication of adenoviral DNA in vitro. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):731–740. doi: 10.1101/sqb.1983.047.01.084. [DOI] [PubMed] [Google Scholar]
  14. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  15. Nagata K., Guggenheimer R. A., Enomoto T., Lichy J. H., Hurwitz J. Adenovirus DNA replication in vitro: identification of a host factor that stimulates synthesis of the preterminal protein-dCMP complex. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6438–6442. doi: 10.1073/pnas.79.21.6438. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Nagata K., Guggenheimer R. A., Hurwitz J. Adenovirus DNA replication in vitro: synthesis of full-length DNA with purified proteins. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4266–4270. doi: 10.1073/pnas.80.14.4266. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Nagata K., Guggenheimer R. A., Hurwitz J. Specific binding of a cellular DNA replication protein to the origin of replication of adenovirus DNA. Proc Natl Acad Sci U S A. 1983 Oct;80(20):6177–6181. doi: 10.1073/pnas.80.20.6177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ostrove J. M., Rosenfeld P., Williams J., Kelly T. J., Jr In vitro complementation as an assay for purification of adenovirus DNA replication proteins. Proc Natl Acad Sci U S A. 1983 Feb;80(4):935–939. doi: 10.1073/pnas.80.4.935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Rawlins D. R., Rosenfeld P. J., Wides R. J., Challberg M. D., Kelly T. J., Jr Structure and function of the adenovirus origin of replication. Cell. 1984 May;37(1):309–319. doi: 10.1016/0092-8674(84)90327-1. [DOI] [PubMed] [Google Scholar]
  20. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Shortle D., Nathans D. Local mutagenesis: a method for generating viral mutants with base substitutions in preselected regions of the viral genome. Proc Natl Acad Sci U S A. 1978 May;75(5):2170–2174. doi: 10.1073/pnas.75.5.2170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Siebenlist U., Hennighausen L., Battey J., Leder P. Chromatin structure and protein binding in the putative regulatory region of the c-myc gene in Burkitt lymphoma. Cell. 1984 Jun;37(2):381–391. doi: 10.1016/0092-8674(84)90368-4. [DOI] [PubMed] [Google Scholar]
  23. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  24. Stillman B. W. The replication of adenovirus DNA with purified proteins. Cell. 1983 Nov;35(1):7–9. doi: 10.1016/0092-8674(83)90201-5. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Wallace R. B., Johnson M. J., Suggs S. V., Miyoshi K., Bhatt R., Itakura K. A set of synthetic oligodeoxyribonucleotide primers for DNA sequencing in the plasmid vector pBR322. Gene. 1981 Dec;16(1-3):21–26. doi: 10.1016/0378-1119(81)90057-3. [DOI] [PubMed] [Google Scholar]
  27. van Bergen B. G., van der Vliet P. C. Temperature-sensitive initiation and elongation of adenovirus DNA replication in vitro with nuclear extracts from H5ts36-, H5ts149-, and H5ts125-infected HeLa cells. J Virol. 1983 May;46(2):642–648. doi: 10.1128/jvi.46.2.642-648.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]

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