An Analysis of Chromatin Structure and Gene Regulation

  • Robert J. Ferl
  • Anna-Lisa Paul
  • Mohammed Ashraf
  • Scott Bollinger
Part of the Basic Life Sciences book series (BLSC, volume 41)


We present here a compilation of our studies aimed at describing the architecture of the maize alcohol dehydrogenase genes (Adh). Specifically, we have sought a structural description of these genes at levels beyond primary sequence; i.e., the association of the DNA with nuclear proteins to form chromatin and the conformation of the DNA itself. The basic definition of chromatin is quite broad and refers to the nuclear DNA together with its associated histones and nonhistone chromosomal proteins in the complex structural array that packages and organizes the eukaryotic genome within the nucleus. What we hope to accomplish by elucidating the structural aspects of the Adh genes is an understanding of the mechanics involved in organizing these genes within the chromatin array, the structural changes involved in preparing the gene for transcriptional activation, and the identification of those sequences in the promoters of these genes that are responsible for regulating transcriptional activity.

We have chosen the maize Adh gene system for analysis for several reasons. First, both Adhl and Adh2 are genetically well-characterized genes that have been cloned and sequenced (5,6,18,37). Second, both genes are transcriptionally induced by anaerobic stress, providing a convenient laboratory mechanism for controlling the transcriptional state of the genes (14). Third, while similarly (though not identically) responsive to anaerobic stress, there is almost no sequence homology between the 5’ flanking regions of the genes (5,6). These two genes, therefore, provide an interesting system to search for similarities and contrasts in their chromatin structure and to elucidate the roles that chromatin structure might play in their coordinate regulation.


Chromatin Structure Heat Shock Gene Hypersensitive Site Sensitive Site Anaerobic Stress 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Aldrich, H.C., D. Akin, M. Hils, and R.J. Ferl (1985) Ultrastructural correlations of anaerobic stress. Tissue and Cell 17: 341–348.PubMedCrossRefGoogle Scholar
  2. 2.
    Burch, J.B.E., and H. Weintraub (1983) Temporal order of chromatin structural changes associated with the activation of the major chicken vitellogenin gene. Cell 33: 65–76.PubMedCrossRefGoogle Scholar
  3. 3.
    Cantor, C. (1981) DNA choreography. Cell 25: 293–295.PubMedCrossRefGoogle Scholar
  4. 4.
    Cantor, C., and A. Efstratiadis (1984) Possible structures of homopurine-homopyrimidine Si hypersensitive sites. Nucl. Acids Res. 12: 8059–8072.Google Scholar
  5. 5.
    Dennis, E.S., M.M. Sachs, W.L. Gerlach, E.J. Finnegan, and W.K. Peacock (1985) Molecular analysis of the alcohol dehydrogenase-2 (Adh2) gene of maize. Nucl. Acids Res. 13: 727–743.Google Scholar
  6. 6.
    Dennis, E.S., W.L. Gerlach, A.J. Pryor, A. Bennetzen, A. Ingils, D. Llewellyn, M.M. Sachs, R.J. Ferl, and W.J. Peacock (1984) Molecular analysis of the alcohol dehydrogenase (Adhl) gene of maize. Nucl. Acids Res. 12: 3983–3989.Google Scholar
  7. 7.
    Elgin, S.C.R. (1984) Anatomy of hypersensitive sites. Nature (London) 309: 213–214.CrossRefGoogle Scholar
  8. 8.
    Emerson, B.M., and G. Felsenfeld (1984) Specific factor conferring nuclease hypersensitivity of the 5’ end of the adult beta-globin gene. Proc. Natl. Acad. Sci., USA 81: 95–99.Google Scholar
  9. 9.
    Evans, T., E. Schon, G. Gora-Maslak, J. Patterson, and A. Efstratiadis (1984) S1 hypersensitive sites in eukaryotic promoter regions. Nucl. Acids Res. 12: 8043–8058.Google Scholar
  10. 10.
    Ferl, R.J. (1985) Modulation of chromatin structure in the regulation of the maize Adhl gene. Mol. Gen. Genet. 200: 207–210.Google Scholar
  11. 11.
    Ferl, R., M. Brennen, and D. Schwartz (1981) In vitro translation of maize ADH: Evidence for the anaerobic induction of mRNA. Biochem. Genet. 18: 681–691.Google Scholar
  12. 12.
    Ferl, R.J., H. Nick, and B. Laughner (1986) S1 nuclease features of the maize alcohol dehydrogenase-1 gene promoter. Plant Mol. Biol. (submitted for publication).Google Scholar
  13. 13.
    Finer, M.H., E.J.B. Fodor, H. Boedtker, and P. Doty (1984) Endonuclease S1 sensitive site in chicken pro-a2(I) collagen 5’ flanking gene region. Proc. Natl. Acad. Sci., USA 81: 1659–1663.Google Scholar
  14. 14.
    Freeling, M. (1973) Simultaneous induction by anaerobiosis or 2,4-D of multiple enzymes specified by two unlinked genes: Differential Adhl Adh2 expression in maize. Mol. Gen. Genet. 127: 215–227.Google Scholar
  15. 15.
    Freeling, M. (1974) Dimerization of multiple maize ADH studied in vivo and in vitro. Biochem. Genet. 12: 407–417.Google Scholar
  16. 16.
    Fritton, H.P., T. Igo-Kemenes, J. Nowock, U. Strech-Jurk, M. Thiesen, and A.E. Sippel (1984) Alternative sets of DNase I hypersensitive sites characterize the various functional states of the chicken lysozyme gene. Nature (London) 311: 163–165.CrossRefGoogle Scholar
  17. 17.
    Garel, A., and R. Axel (1976) Selective digestion of transcriptionally active ovalbumin genes from oviduct nuclei. Proc. Natl. Acad. Sci., USA 73: 3966–3970.Google Scholar
  18. 18.
    Gerlach, W.L., A.J. Pryor, E.S. Dennis, R.J. Ferl, M.M. Sachs, and W.J. Peacock (1982) cDNA cloning and induction of the alcohol dehydrogenase gene (Adhl) of maize. Proc. Natl. Acad. Sci., USA 79: 29812985.Google Scholar
  19. 19.
    Glikin, G.H., G. Gargiulo, L. Rena-Descalzi, and A. Worcel (1983) Escherichia coli single-strand binding protein stabilizes specific denatured sites in superhelical DNA. Nature (London) 303: 770–774.CrossRefGoogle Scholar
  20. 20.
    Johnson, B., and A. Rich (1985) Chemical probes of DNA conformation: Detection of Z-DNA at nucleotide resolution. Cell 42: 713–724.Google Scholar
  21. 21.
    Jongstra, J., T.R. Reudelhuber, P. Oudet, C. Benoist, C.-B. Chae, J.M. Jeltsch, D.J. Mathis, and P. Chambon (1984) Induction of altered chromatin structures by Simian Virus 40 enhancer promoter elements. Nature (London) 307: 708–714.CrossRefGoogle Scholar
  22. 22.
    Kaye, J.S., S. Pratt-Kaye, M. Bellard, G. Dretzen, F. Bellard, and P. Chambon (1986) Steroid hormone dependence of four DNase I-hypersensitive regions located within the 7000-bp 5’-flanking segment of the ovalbumin gene. EMBO J. 5: 277–285.PubMedGoogle Scholar
  23. 23.
    Keene, M.A., V. Corces, K. Lowenhaupt, and S.C.R. Elgin (1981) DNase I hypersensitive sites in Drosophila chromatin occur at the 5’ ends of regions of transcription. Proc. Natl. Acad. Sci., USA 78: 143–146.Google Scholar
  24. 24.
    Koo, H.-S., H.-M. Wu, and D.M. Crother (1986) DNA bending at adenine-thymine tracts. Nature (London) 320: 501–506.CrossRefGoogle Scholar
  25. 25.
    Larsen, A., and H. Weintraub (1982) An altered conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell 29: 609–622.PubMedCrossRefGoogle Scholar
  26. 26.
    Mace, H.A.F., H.R.B. Pelham, and A. Travers (1983) Association of an S1 nuclease sensitive structure with short direct repeats 5’ of Drosophila heat shock genes. Nature (London) 304: 555–557.CrossRefGoogle Scholar
  27. 27.
    Margot, J.B., and R.C. Hardison (1985) DNase-1 and nuclease S1 sensitivity of the rabbit B1 globin gene in nuclei and in supercoiled plastids. J. Mol. Biol. 184: 195–210.Google Scholar
  28. 28.
    McKeon, C., A. Schmidt, and B. deCrombrugghe (1984) A sequence conserved in both the chicken and mouse a2(I) collagen promoter contains sites sensitive to S1 nuclease. J. Biol. Chem. 259: 6636–6640.Google Scholar
  29. 29.
    Murray, M.G., and W.C. Kennard (1984) Altered chromatin conformation of higher plant gene phaseolin. Biochemistry 23: 4225–4232.CrossRefGoogle Scholar
  30. 30.
    Nelson, J.A., and M. Groudine (1986) Transcriptional regulation of the human cytomegalovirus major immediate-early gene is associated with induction of DNase I-hypersensitive sites. Mol. Cell. Biol. 6: 452461.Google Scholar
  31. 31.
    Nickol, J.M., and G. Felsenfeld (1983) DNA conformation at the 5’ end of the chicken adult B-globin gene. Cell 35: 467–477.PubMedCrossRefGoogle Scholar
  32. 32.
    Nordheim, A., and A. Rich (1983) Negatively supercoiled Simian Virus 40 DNA contains Z-DNA segments within the transcriptional enhancer region. Nature (London) 303: 674–679.CrossRefGoogle Scholar
  33. 33.
    Parker, C.S., and J. Topol (1984) A Drosophila RNA polymerase II transcription factor contains a promoter-region-specific DNA binding activity. Cell 36: 357–369.PubMedCrossRefGoogle Scholar
  34. 34.
    Parker, C.S., and J. Topol (1984) A Drosophila RNA polymerase II transcription factor contains a promoter-region-specific DNA binding activity. Cell 36: 357–369.PubMedCrossRefGoogle Scholar
  35. 35.
    Pospelov, V.A., G.H. Klobeck, and G.H. Zachau (1984) Correlation between DNase I hypersensitive sites and putative regulatory sequences in human immunoglobulin genes of the K light chain type. Nucl. Acids Res. 12: 7007–7021.Google Scholar
  36. 36.
    Schon, E., T. Evans, J. Welsh, and A. Efstratiadis (1983) Conformation of promoter DNA: Fine mapping of S1 hypersensitive sites. Cell 35: 837–848.PubMedCrossRefGoogle Scholar
  37. 37.
    Schwartz, D. (1966) The genetic control of alcohol dehydrogenase in maize: Gene duplication and repression. Proc. Natl. Acad. Sci., USA 56: 1431–1436.Google Scholar
  38. 38.
    Senear, A.W., and R.D. Palmiter (1983) Expression of mouse metallothionein-1 gene alters the nuclease hypersensitivity of its 5’ regulatory region. Cold Spring Harbor Symp. Quant. Biol. 47: 539–547.Google Scholar
  39. 39.
    Shermoen, A.W., and S.K. Beckendorf (1982) A complex of interacting DNase I-hypersensitive sites near the Drosophila glue protein gene Sgs4. Cell 29: 601–607.PubMedCrossRefGoogle Scholar
  40. 40.
    Singleton, C., M. Kilpatrick, and R. Wells (1984) S1 nuclease recognizes DNA conformational junction between left-handed helical (dT-dG)n.(dC-dA)n and contiguous right-handed sequences. J. Biol. Chem. 259: 1963–1967.Google Scholar
  41. 41.
    Sledziewski, A., and E.T. Young (1982) Chromatin conformational changes accompany transcriptional activation of a glucose-repressed gene in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci., USA 79: 253256.Google Scholar
  42. 42.
    Sunter, G., K.W. Buck, and R.H.A. Coutts (1985) S1-sensitive sites in the supercoiled double stranded form of tomato golden mosaic virus DNA component B: Identification of regions of potential alternative secondary structure and regulatory function. Nucl. Acids Res. 13: 4645–4659.Google Scholar
  43. 43.
    Thomas, G.H., E. Siegfried, and S.C.R. Elgin (1985) DNase I hypersensitive sites: A structural feature of chromatin associated with gene expression. In Chromosomal Proteins and Gene Expression, G. Reeck, G. Goodwin, and P. Puigdomench, eds. Plenum Press, New York, pp. 77–101.CrossRefGoogle Scholar
  44. 44.
    Vasil, V., and I.K. Vasil (1986) Plant regeneration from friable embryogenic callus and cell suspension cultures of Zea mays. J. Plant Physiol. 124: 399–408.CrossRefGoogle Scholar
  45. 45.
    Weintraub, H. (1985) High resolution mapping of S1 and DNase I hypersensitive sites in chromatin. Mol. Cell. Biol. 5: 1538–1539.Google Scholar
  46. 46.
    Weintraub, H., and H. Groudine (1976) Chromosome subunits in active genes have an altered conformation. Science 193: 848–856.PubMedCrossRefGoogle Scholar
  47. 47.
    Weisbrod, S. (1982) Active chromatin. Nature (London) 297: 289–295.CrossRefGoogle Scholar
  48. 48.
    Wu, C. (1980) The 5’ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature (London) 286: 854–860.CrossRefGoogle Scholar
  49. 49.
    Wu, C., and W. Gilbert (1981) Tissue specific exposure of chromatin structure at the 5’ terminus of the rat preproinsulin II gene. Proc. Natl. Acad. Sci., USA 78: 1577–1580.Google Scholar
  50. 50.
    Yu, Y.-T., and J.L. Manley (1986) Structure and function of the Si nuclease sensitive site in the adenovirus late promoter. Cell 45: 743–751.Google Scholar
  51. 51.
    Zinn, K., and T. Maniatis (1986) Detection of factors that interact with the human B-interferon regulatory region in vivo by DNase I foot-printing. Cell 45: 611–618.PubMedCrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1987

Authors and Affiliations

  • Robert J. Ferl
    • 1
  • Anna-Lisa Paul
    • 1
  • Mohammed Ashraf
    • 1
  • Scott Bollinger
    • 1
  1. 1.Department of BotanyUniversity of FloridaGainesvilleUSA

Personalised recommendations