Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 Mar 25;17(6):2333–2350. doi: 10.1093/nar/17.6.2333

In vivo protein binding sites and nuclease hypersensitivity in the promoter region of a cell cycle regulated human H3 histone gene.

U Pauli 1, S Chrysogelos 1, H Nick 1, G Stein 1, J Stein 1
PMCID: PMC317599  PMID: 2539585

Abstract

The chromatin structure and protein-DNA interactions of a cell cycle regulated human H3 histone gene have been examined at different levels of resolution. Using traditional Southern blot analysis we have investigated the accessibility of the H3 coding region and its flanking sequences to DNase I, S1 nuclease and restriction endonuclease digestion. Using the native genomic blotting method recently developed in our laboratory, two sites of protein-DNA interaction in the proximal 240 bp of the promoter region of this H3 gene were established. Further in vivo analysis of protein-DNA binding sites in intact cells by genomic sequencing revealed, with single nucleotide resolution, the guanine contacts and footprints of the proteins bound to the promoter. The relative locations of protein-DNA interactions in this H3 gene are similar to those identified in vivo and in vitro in a cell cycle dependent human H4 histone gene. The proteins complexed with the H3 histone gene promoter can be dissociated between 0.16 and 0.28 M NaCl. The protein-DNA contacts persist throughout the cell cycle and thus may have a functional relationship with the basal level of transcription of this H3 gene that occurs during and outside of S phase.

Full text

PDF
2333

Images in this article

2336Image
on p.2336
2337Image
on p.2337
2341Image
on p.2341
2342Image
on p.2342
2343Image
on p.2343

Selected References

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

  1. Baumbach L. L., Marashi F., Plumb M., Stein G., Stein J. Inhibition of DNA replication coordinately reduces cellular levels of core and H1 histone mRNAs: requirement for protein synthesis. Biochemistry. 1984 Apr 10;23(8):1618–1625. doi: 10.1021/bi00303a006. [DOI] [PubMed] [Google Scholar]
  2. Baumbach L. L., Stein G. S., Stein J. L. Regulation of human histone gene expression: transcriptional and posttranscriptional control in the coupling of histone messenger RNA stability with DNA replication. Biochemistry. 1987 Sep 22;26(19):6178–6187. doi: 10.1021/bi00393a034. [DOI] [PubMed] [Google Scholar]
  3. Briggs M. R., Kadonaga J. T., Bell S. P., Tjian R. Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science. 1986 Oct 3;234(4772):47–52. doi: 10.1126/science.3529394. [DOI] [PubMed] [Google Scholar]
  4. Carthew R. W., Chodosh L. A., Sharp P. A. An RNA polymerase II transcription factor binds to an upstream element in the adenovirus major late promoter. Cell. 1985 Dec;43(2 Pt 1):439–448. doi: 10.1016/0092-8674(85)90174-6. [DOI] [PubMed] [Google Scholar]
  5. Chrysogelos S., Pauli U., Stein G., Stein J. Fine mapping of the chromatin structure of a cell cycle-regulated human H4 histone gene. J Biol Chem. 1989 Jan 15;264(2):1232–1237. [PubMed] [Google Scholar]
  6. Chrysogelos S., Riley D. E., Stein G., Stein J. A human histone H4 gene exhibits cell cycle-dependent changes in chromatin structure that correlate with its expression. Proc Natl Acad Sci U S A. 1985 Nov;82(22):7535–7539. doi: 10.1073/pnas.82.22.7535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dailey L., Hanly S. M., Roeder R. G., Heintz N. Distinct transcription factors bind specifically to two regions of the human histone H4 promoter. Proc Natl Acad Sci U S A. 1986 Oct;83(19):7241–7245. doi: 10.1073/pnas.83.19.7241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dynan W. S., Tjian R. Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins. 1985 Aug 29-Sep 4Nature. 316(6031):774–778. doi: 10.1038/316774a0. [DOI] [PubMed] [Google Scholar]
  10. Elgin S. C. The formation and function of DNase I hypersensitive sites in the process of gene activation. J Biol Chem. 1988 Dec 25;263(36):19259–19262. [PubMed] [Google Scholar]
  11. Ephrussi A., Church G. M., Tonegawa S., Gilbert W. B lineage--specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science. 1985 Jan 11;227(4683):134–140. doi: 10.1126/science.3917574. [DOI] [PubMed] [Google Scholar]
  12. Goodbourn S., Burstein H., Maniatis T. The human beta-interferon gene enhancer is under negative control. Cell. 1986 May 23;45(4):601–610. doi: 10.1016/0092-8674(86)90292-8. [DOI] [PubMed] [Google Scholar]
  13. Heintz N., Sive H. L., Roeder R. G. Regulation of human histone gene expression: kinetics of accumulation and changes in the rate of synthesis and in the half-lives of individual histone mRNAs during the HeLa cell cycle. Mol Cell Biol. 1983 Apr;3(4):539–550. doi: 10.1128/mcb.3.4.539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Helms S. R., van Wijnen A. J., Kroeger P., Shiels A., Stewart C., Hirshman J., Stein J. L., Stein G. S. Identification of an enhancer-like element upstream from a cell cycle dependent human H4 histone gene. J Cell Physiol. 1987 Sep;132(3):552–558. doi: 10.1002/jcp.1041320319. [DOI] [PubMed] [Google Scholar]
  15. Hentschel C. C., Birnstiel M. L. The organization and expression of histone gene families. Cell. 1981 Aug;25(2):301–313. doi: 10.1016/0092-8674(81)90048-9. [DOI] [PubMed] [Google Scholar]
  16. Jones K. A., Kadonaga J. T., Luciw P. A., Tjian R. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. Science. 1986 May 9;232(4751):755–759. doi: 10.1126/science.3008338. [DOI] [PubMed] [Google Scholar]
  17. Kroeger P., Stewart C., Schaap T., van Wijnen A., Hirshman J., Helms S., Stein G., Stein J. Proximal and distal regulatory elements that influence in vivo expression of a cell cycle-dependent human H4 histone gene. Proc Natl Acad Sci U S A. 1987 Jun;84(12):3982–3986. doi: 10.1073/pnas.84.12.3982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Larsen A., Weintraub H. An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell. 1982 Jun;29(2):609–622. doi: 10.1016/0092-8674(82)90177-5. [DOI] [PubMed] [Google Scholar]
  19. Lenardo M., Pierce J. W., Baltimore D. Protein-binding sites in Ig gene enhancers determine transcriptional activity and inducibility. Science. 1987 Jun 19;236(4808):1573–1577. doi: 10.1126/science.3109035. [DOI] [PubMed] [Google Scholar]
  20. Marashi F., Helms S., Shiels A., Silverstein S., Greenspan D. S., Stein G., Stein J. Enhancer-facilitated expression of prokaryotic and eukaryotic genes using human histone gene 5' regulatory sequences. Biochem Cell Biol. 1986 Apr;64(4):277–289. doi: 10.1139/o86-039. [DOI] [PubMed] [Google Scholar]
  21. McGhee J. D., Wood W. I., Dolan M., Engel J. D., Felsenfeld G. A 200 base pair region at the 5' end of the chicken adult beta-globin gene is accessible to nuclease digestion. Cell. 1981 Nov;27(1 Pt 2):45–55. doi: 10.1016/0092-8674(81)90359-7. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. Nick H., Gilbert W. Detection in vivo of protein-DNA interactions within the lac operon of Escherichia coli. 1985 Feb 28-Mar 6Nature. 313(6005):795–798. doi: 10.1038/313795a0. [DOI] [PubMed] [Google Scholar]
  24. Parish R. W., Banz E., Ness P. J. Methidiumpropyl-EDTA-iron(II) cleavage of ribosomal DNA chromatin from Dictyostelium discoideum. Nucleic Acids Res. 1986 Mar 11;14(5):2089–2107. doi: 10.1093/nar/14.5.2089. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Parker C. S., Topol J. A Drosophila RNA polymerase II transcription factor contains a promoter-region-specific DNA-binding activity. Cell. 1984 Feb;36(2):357–369. doi: 10.1016/0092-8674(84)90229-0. [DOI] [PubMed] [Google Scholar]
  26. Pauli U., Chrysogelos S., Stein G., Stein J., Nick H. Protein-DNA interactions in vivo upstream of a cell cycle-regulated human H4 histone gene. Science. 1987 Jun 5;236(4806):1308–1311. doi: 10.1126/science.3035717. [DOI] [PubMed] [Google Scholar]
  27. Pauli U., Chrysogelos S., Stein J., Stein G. Native genomic blotting: a novel approach to mapping DNase I hypersensitive sites and protein-DNA interactions at high resolution. Biotechniques. 1988 Feb;6(2):142–147. [PubMed] [Google Scholar]
  28. Pauli U., Chrysogelos S., Stein J., Stein G. Native genomic blotting: high-resolution mapping of DNase I-hypersensitive sites and protein-DNA interactions. Proc Natl Acad Sci U S A. 1988 Jan;85(1):16–20. doi: 10.1073/pnas.85.1.16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Plumb M., Stein J., Stein G. Influence of DNA synthesis inhibition on the coordinate expression of core human histone genes during S phase. Nucleic Acids Res. 1983 Nov 25;11(22):7927–7945. doi: 10.1093/nar/11.22.7927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Reed K. C., Mann D. A. Rapid transfer of DNA from agarose gels to nylon membranes. Nucleic Acids Res. 1985 Oct 25;13(20):7207–7221. doi: 10.1093/nar/13.20.7207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Reeves R. Transcriptionally active chromatin. Biochim Biophys Acta. 1984 Sep 10;782(4):343–393. doi: 10.1016/0167-4781(84)90044-7. [DOI] [PubMed] [Google Scholar]
  32. Sawadogo M., Roeder R. G. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell. 1985 Nov;43(1):165–175. doi: 10.1016/0092-8674(85)90021-2. [DOI] [PubMed] [Google Scholar]
  33. Schümperli D. Cell-cycle regulation of histone gene expression. Cell. 1986 May 23;45(4):471–472. doi: 10.1016/0092-8674(86)90277-1. [DOI] [PubMed] [Google Scholar]
  34. Sierra F., Lichtler A., Marashi F., Rickles R., Van Dyke T., Clark S., Wells J., Stein G., Stein J. Organization of human histone genes. Proc Natl Acad Sci U S A. 1982 Mar;79(6):1795–1799. doi: 10.1073/pnas.79.6.1795. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Singh H., Sen R., Baltimore D., Sharp P. A. A nuclear factor that binds to a conserved sequence motif in transcriptional control elements of immunoglobulin genes. Nature. 1986 Jan 9;319(6049):154–158. doi: 10.1038/319154a0. [DOI] [PubMed] [Google Scholar]
  36. SivaRaman L., Subramanian S., Thimmappaya B. Identification of a factor in HeLa cells specific for an upstream transcriptional control sequence of an EIA-inducible adenovirus promoter and its relative abundance in infected and uninfected cells. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5914–5918. doi: 10.1073/pnas.83.16.5914. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. 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]
  38. Stalder J., Larsen A., Engel J. D., Dolan M., Groudine M., Weintraub H. Tissue-specific DNA cleavages in the globin chromatin domain introduced by DNAase I. Cell. 1980 Jun;20(2):451–460. doi: 10.1016/0092-8674(80)90631-5. [DOI] [PubMed] [Google Scholar]
  39. Stein G. S., Borun T. W. The synthesis of acidic chromosomal proteins during the cell cycle of HeLa S-3 cells. I. The accelerated accumulation of acidic residual nuclear protein before the initiation of DNA replication. J Cell Biol. 1972 Feb;52(2):292–307. doi: 10.1083/jcb.52.2.292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wells D. E. Compilation analysis of histones and histone genes. Nucleic Acids Res. 1986;14 (Suppl):r119–r149. doi: 10.1093/nar/14.suppl.r119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Wu C. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature. 1980 Aug 28;286(5776):854–860. doi: 10.1038/286854a0. [DOI] [PubMed] [Google Scholar]
  42. Wu C. Two protein-binding sites in chromatin implicated in the activation of heat-shock genes. Nature. 1984 May 17;309(5965):229–234. doi: 10.1038/309229a0. [DOI] [PubMed] [Google Scholar]
  43. Yang J. Q., Remmers E. F., Marcu K. B. The first exon of the c-myc proto-oncogene contains a novel positive control element. EMBO J. 1986 Dec 20;5(13):3553–3562. doi: 10.1002/j.1460-2075.1986.tb04682.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Zinn K., Maniatis T. Detection of factors that interact with the human beta-interferon regulatory region in vivo by DNAase I footprinting. Cell. 1986 May 23;45(4):611–618. doi: 10.1016/0092-8674(86)90293-x. [DOI] [PubMed] [Google Scholar]
  45. van Wijnen A. J., Stein J. L., Stein G. S. A nuclear protein with affinity for the 5' flanking region of a cell cycle dependent human H4 histone gene in vitro. Nucleic Acids Res. 1987 Feb 25;15(4):1679–1698. doi: 10.1093/nar/15.4.1679. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES