Skip to main content

Some Observations on DNA Structure and Chromatin Organization at Specific Loci in Drosophila melanogaster

  • Chapter
Eukaryotic Gene Expression

Abstract

Within the eukaryotic nucleus, the DNA is packaged in a complex fashion by association with histones and other chromosomal proteins. One may suggest a priori that differential protein packaging of coding sequences at the broad level of the chromomere, or in the specific vicinity of a gene, or both, might be an important determinant in the selective expression of these sequences. Our goals have been to map features of chromatin structure relative to known functional sequences, to establish the presence of alternative patterns of structure during development, and to look for alterations in structure that might occur as part of the process of gene induction and repression. To this end, we have recently conducted a series of studies utilizing several different DNA-cleavage reagents to examine the patterns of DNA-protein interaction at a number of Drosophila genes. Concurrent studies using immunofluorescent staining of polytene chromosomes have identified several presumptive structural nonhistone chromosomal proteins, including some the distribution pattern of which indicates a preferential association with loci that are to be expressed at some point in the development of the salivary gland cells of Drosophila. We anticipate that the synthesis of this information may ultimately lead to a better understanding of the process of gene activation and hence provide insights into the regulation of this event during development. For a more thorough review of many of the issues raised herein, see Cartwright et al. (1982).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Armstrong, K., and Bauer, W. R., 1982, Preferential site-dependent cleavage by restriction endonuclease Pst I, Nucleic Acids Res. 10: 993–1007.

    Article  PubMed  CAS  Google Scholar 

  • Ashburner, M., and Bonner, J. J., 1979, The induction of gene activity in Drosophila by heat shock, Cell 17: 241–254.

    Article  PubMed  CAS  Google Scholar 

  • Bellard, M., Dretgen, G., Bellard, F., Oudet, P., and Chambon, P., 1982, Disruption of the typical chromatin structure in a 2500 base-pair region at the 5’ end of the actively transcribed ovalbumin gene, Eur. Mol. Biol. Assoc. J. 1: 223–230.

    CAS  Google Scholar 

  • Bloom, K. S., and Anderson, J. N., 1979, Conformation of ovalbumin and globin genes in chromatin during differential gene expression, J. Biol. Chem. 254: 10532–10539.

    PubMed  CAS  Google Scholar 

  • Bloom, K. S., and Carbon, J., 1982, Yeast centromere DNA is a unique and highly ordered structure in chromosomes and small circular minichromosomes, Cell 29: 305–317.

    Article  PubMed  CAS  Google Scholar 

  • Borchsenius, S., Bonven, B., Leer, J. C., and Westergaard, O., 1981, Nuclease-sensitive regions on the extrachromosomal r-chromatin from Tetrahymena pyriformis, Eur. J. Biochem. 117: 245–250.

    Article  PubMed  CAS  Google Scholar 

  • Bryan, P. N., Hofstetter, H., and Birnstiel, M. L., 1981, Nucleosome arrangement on rRNA genes of Xenopus laevis, Cell 27: 459–466.

    Article  PubMed  CAS  Google Scholar 

  • Cartwright, I. L., and Elgin, S. C. R., 1982, Analysis of chromatin structure and DNA sequence organization: Use of the 1,10-phenanthroline—cuprous complex, Nucleic Acids Res. 10: 5835–5853.

    Article  PubMed  CAS  Google Scholar 

  • Cartwright, I. L., Keene, M. A., Howard, G. C., Abmayr, S. M., Fleischmann, G., Lowenhaupt, K., and Elgin, S. C. R., 1982, Chromatin structure and gene activity: The role of nonhistone chromosomal proteins, CRC Crit. Rev. Biochem. 13: 1–86.

    Article  PubMed  CAS  Google Scholar 

  • Cartwright, I. L., Hertzberg, R. P., Dervan, P. B., and Elgin, S. C. R., 1983, Cleavage of chromatin with (methidiumpropyl-EDTA) iron (II) Proc. Natl. Acad. Sci. USA 80: 3213–3217.

    Article  PubMed  CAS  Google Scholar 

  • Chao, M. V., Gralla, J., and Martinson, H. G., 1979, DNA sequence directs placement of histone cores on restriction fragments during nucleosome formation, Biochemistry 18: 1068–1074.

    Article  PubMed  CAS  Google Scholar 

  • Chao, M. V., Gralla, J. D., and Martinson, H., 1980, lac operator nucleosomes. 1. Repressor binds specifically to operator within the nucleosome core, Biochemistry 19: 3254–3260.

    Google Scholar 

  • Dickerson, R. E., and Drew, H. R., 1981a, Kinematic model for B-DNA, Proc. Natl. Acad. Sci. U.S.A. 78: 7318–7322.

    Article  PubMed  CAS  Google Scholar 

  • Dickerson, R. E., and Drew, H. R., 198 lb, Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure, J. Mol. Biol. 149: 761–786.

    Google Scholar 

  • Dunn, K., and Griffith, J. D., 1980, The presence of RNA in a double helix inhibits its interaction with histone protein, Nucleic Acids Res. 8: 555–572.

    Article  PubMed  CAS  Google Scholar 

  • Elgin, S. C. R., 1981, Minireview: DNAase I-hypersensitive sites of chromatin, Cell 27: 413–415.

    Article  PubMed  CAS  Google Scholar 

  • Elgin, S. C. R., Serunian, L. A., and Silver, L. M., 1978, Distribution patterns of Drosophila nonhistone chromosomal proteins, Cold Spring Harbor Symp. Quant. Biol. 42: 839–850.

    Article  PubMed  CAS  Google Scholar 

  • Elgin, S. C. R., Cartwright, I. L., Fleischmann, G., Lowenhaupt, K., and Keene, M. A., 1983, Cleavage reagents as probes of DNA sequence organization and chromatin structure: Drosophila melanogaster locus 67B1, Cold Spring Harbor Symp. Quant. Biol. 47: 529–538.

    Article  PubMed  Google Scholar 

  • Garel, A., Zolan, M., and Axel, R., 1977, Genes transcribed at diverse rates have a similar conformation in chromatin, Proc. Natl. Acad. Sci. U.S.A. 74: 4867–4871.

    Article  PubMed  CAS  Google Scholar 

  • Hertzberg, R. P., and Dervan, P. B., 1982, Cleavage of double helical DNA by (methidiumpropyl-EDTA) iron (II), J. Am. Chem. Soc. 104: 313–315.

    Article  CAS  Google Scholar 

  • Hörz, W., and Altenberger, W., 1981, Sequence specific cleavage of DNA by micrococcal nuclease, Nucleic Acids Res. 9: 2643–2658.

    Article  PubMed  Google Scholar 

  • Keene, M. A., and Elgin, S. C. R., 1981, Micrococcal nuclease as a probe of DNA sequence organization and chromatin structure, Cell 27: 57–64.

    Article  PubMed  CAS  Google Scholar 

  • Keene, M. A., and Elgin, S. C. R., 1982, Perturbations of chromatin structure associated with gene expression, in: Heat Shock: From Bacteria to Man ( M. J. Schlesinger, M. Ashburner, and A. Tissieres, eds.), Cold Spring Harbor Laboratory, New York, pp. 83–90.

    Google Scholar 

  • Keene, M. A., and Elgin, S. C. R., 1984, Patterns of DNA structural polymorphism and their evolutionary implications (submitted).

    Google Scholar 

  • Keene, M. A., Corces, V., Lowenhaupt, K., and Elgin, S. C. R., 1981, DNase I hypersensitive sites in Drosophila chromatin occur at the 5 ends of regions of transcription, Proc. Nad. Acad. Sci. U.S.A. 78: 143–146.

    Article  CAS  Google Scholar 

  • Kunkel, G. R., and Martinson, H. G., 1981, Nucleosomes will not form on double-stranded RNA or over poly(dA) poly(dT) tracts in recombinant DNA, Nucleic Acids Res. 9: 6869–6888.

    Article  PubMed  CAS  Google Scholar 

  • Kuo, M. T., Mandel, J. L., and Chambon, P., 1979, DNA methylation: Correlation with DNase I sensitivity of chicken ovalbumin and conalbumin chromatin, Nucleic Acids Res. 7: 2105–2114.

    Article  PubMed  CAS  Google Scholar 

  • Larsen, A., and Weintraub, H., 1982, An altered DNA conformation detected by Si nuclease occurs at specific regionsin active chick globin chromatin, Cell 29: 609–622.

    Article  PubMed  CAS  Google Scholar 

  • Lawson, G. M., Knoll, B. J., March, C. J., Woo, S. L. C., Tsai, J.-J., and O’Malley, B. W., 1982, Definition of 5’ and 3’ structural boundaries of the chromatin domain containing the ovalbumin multigene family, J. Biol. Chem. 257: 1501–1557.

    PubMed  CAS  Google Scholar 

  • Lomonossoff, G. P., Butler, P. J. G., and Klug, A., 1981, Sequence-dependent variation in the conformation of DNA, J. Mol. Biol. 149: 745–760.

    Article  PubMed  CAS  Google Scholar 

  • Lowenhaupt, K., Keene, M. A., Cartwright, I. L., and Elgin, S. C. R., 1983a, Chromatin structure of eukaryotic genes: DNase I hypersensitive sites, Stadler Genet. Symp. 14 (in press).

    Google Scholar 

  • Lowenhaupt, K., Cartwright, I. L., Keene, M. A., Zimmerman, J. L., and Elgin, S. C. R., 1983b, Chromatin structure in pre-and postblastula embryos of Drosophila, Dey. Biol. 99: 194–201.

    Article  CAS  Google Scholar 

  • Marshall, L. E., Graham, D. R., Reich, K. A., and Sigman, D. S., 1981, Cleavage of deoxyribonucleic acid by the 1,10-phenanthroline—cuprous complex: Hydrogen peroxide requirement and primary and secondary structure specificity, Biochemistry 20: 244–250.

    Article  PubMed  CAS  Google Scholar 

  • Mayfield, J. E., Serunian, L. A., Silver, L. M., and Elgin, S. C. R., 1978, A protein released by DNase I digestion of Drosophila nuclei is preferentially associated with puffs, Cell 14: 539–544.

    Article  PubMed  CAS  Google Scholar 

  • McGhee, J. D., Wood, W. I., Dolan, M., Engel, J. D., and Felsenfeld, G., 1981, A 200 base pair region at the 5’ end of the chicken adult 0-globin gene is accessible to nuclease digestion, Cell 27: 45–55.

    Article  PubMed  CAS  Google Scholar 

  • Muskavitch, M., and Hogness, D. S., 1980, Molecular analysis of a gene in a developmentally regulated puff of Drosophila melanogaster, Proc. Natl. Acad. Sci. U.S.A. 77: 7362–7366.

    Article  PubMed  CAS  Google Scholar 

  • Muskavitch, M. A. T., and Hogness, D. S., 1982, An expandable gene that encodes a Drosophila glue protein is not expressed in variants lacking remote upstream sequences, Cell 29: 1041–1051.

    Article  PubMed  CAS  Google Scholar 

  • Nasmyth, K. A., 1982, The regulation of yeast mating-type chromatin structure by SIR: An action at a distance affecting both transcription and transposition, Cell 30: 567–578.

    Article  PubMed  CAS  Google Scholar 

  • Nedospasov, S. A., and Georgiev, G. P., 1980, Non-random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease, Biochem. Biophys. Res. Commun. 92: 532–539.

    Article  PubMed  CAS  Google Scholar 

  • Nickol, J., Behe, M., and Felsenfeld, G., 1982, Effect of the B—Z transition in poly(dG m5dC) poly(dG m5dC) on nucleosome formation, Proc. Natl. Acad. Sci. U.S.A. 79: 1771–1775.

    Article  PubMed  CAS  Google Scholar 

  • Palen, T., Gottschling, D. S., and Cech, T., 1982, Transcribed and non-transcribed regions of the ribosomal RNA gene of Tetrahymena exhibit different chromatin structures, J. Cell Biochem. Suppl. 6: 336.

    Google Scholar 

  • Palmiter, R. D., Mulvihill, E. R., McKnight, G. S., and Senear, A. W., 1978, Regulation of gene expression in the chick oviduct by steroid hormones, Cold Spring Harbor Symp. Quant. Biol. 42: 639–648.

    Article  PubMed  CAS  Google Scholar 

  • Peck, L. J., and Wang, J. C., 1981, Sequence dependence of the helical repeat of DNA in solution, Nature (London) 292: 375–378.

    Article  CAS  Google Scholar 

  • Que, B. G., Downey, K. M., and So, A. G., 1980, Degradation of deoxyribonucleic acid by a 1,10-phenanthroline-copper complex: The role of hydroxyl radicals, Biochemistry 19: 5987–5991.

    Article  PubMed  CAS  Google Scholar 

  • Rhodes, D., and Klug, A., 1981, Sequence-dependent helical periodicity of DNA, Nature (London) 292: 378–380.

    Article  CAS  Google Scholar 

  • Samal, B., Worcel, A., Louis, C., and Schedi, P., 1981, Chromatin structure of the histone genes of D. melanogaster, Cell 23: 401–410.

    Article  PubMed  CAS  Google Scholar 

  • Saragosti, S., Moyne, G., and Yaniv, M., 1980, Absence of nucleosomes in a fraction of SV40 chromatin between the origin of replication and the region coding for the late leader RNA, Cell 20: 65–75.

    Article  PubMed  CAS  Google Scholar 

  • Selleck, S. B., Elgin, S. C. R., and Cartwright, I. L., 1984, Supercoil-dependent features of DNA structure at Drosophila locus 67B1 (submitted).

    Google Scholar 

  • Sheffery, M., Rifkind, R. A., and Marks, P. A., 1982, Murine erythroleukemia cell differentiation: DNase I hypersensitivity and DNA methylation near the globin genes, Proc. Natl. Acad. Sci. U.S.A. 79: 1180–1184.

    Article  PubMed  CAS  Google Scholar 

  • Shermoen, A. W., and Beckendorf, S. K., 1982, A complex of interacting DNase I-hypersensitive sites near the Drosophila glue protein gene, Sgs 4, Cell 29: 601–607.

    Article  PubMed  CAS  Google Scholar 

  • Silver, L. M., and Elgin, S. C. R., 1976, A method for determination of the in situ distribution of chromosomal proteins, Proc. Natl. Acad. Sci. U.S.A. 73: 423–427.

    Article  PubMed  CAS  Google Scholar 

  • Silver, L. M., and Elgin, S. C. R., 1978, Immunological analysis of protein distributions in Drosophila polytene chromosomes, in: The Cell Nucleus V: Chromatin, Part B ( H. Busch, ed.), Academic Press, New York, pp. 216–263.

    Google Scholar 

  • Sirotkin, K., and Davidson, N., 1982, Developmentally regulated transcription from Drosophila melanogaster chromosomal site 67B, Dev. Biol. 89: 196–210.

    Article  PubMed  CAS  Google Scholar 

  • Sledziewski, A., and Young, E. T., 1982, Chromatin conformational changes accompany transcriptional activation of a glucose-repressed gene in Saccharomyces cerevisae, Proc. Natl. Acad. Sci. U.S.A. 79: 253–256.

    Article  PubMed  CAS  Google Scholar 

  • Southern, E. M., 1975, Detection of specific sequences among DNA fragments separated by gel electrophoresis, J. Mol. Biol. 98: 503–517.

    Article  PubMed  CAS  Google Scholar 

  • Stalder, J., Larsen, A., Engel, J. D., Dolan, M., Groudine, M., and Weintraub, H., 1980, Tissue-specific DNA cleavages in the globin chromatin domain introduced by DNase I, Cell 20: 451–460.

    Article  PubMed  CAS  Google Scholar 

  • VanDyke, M. W., Hertzberg, R. P., and Dervan, P. B., 1982, Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns with methidiumpropyl-EDTA • Fe(II), Proc. Natl. Acad. Sci. U.S.A. 79: 5470–5474.

    Article  CAS  Google Scholar 

  • Weintraub, H., and Groudine, M., 1976, Chromosomal subunits in active genes have an altered conformation, Science 193: 848–856.

    Article  PubMed  CAS  Google Scholar 

  • Weintraub, H., Larsen, A., and Groudine, M., 1981, Globin-gene switching during the development of chicken embryos: Expression and chromosome structure, Cell 24: 333–344.

    Article  PubMed  CAS  Google Scholar 

  • Weintraub, H., Berg, H., Groudine, M., and Graf, T., 1982, Temperature-sensitive changes in the structure of globin chromatin in lines of red cell precursors transformed by a ts-AEV virus, Cell, 28: 931–940.

    Article  PubMed  CAS  Google Scholar 

  • Wong, Y.-C., O’Connell, P., Rosbash, M., and Elgin, S. C. R., 1981, DNase I hypersensitive sites of the chromatin for Drosophila melanogaster ribosomal protein 49 gene, Nucleic Acids Res. 9: 6749–6762.

    Article  PubMed  CAS  Google Scholar 

  • Wu, C., 1980, The 5’ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I, Nature (London) 286: 854–860.

    Article  CAS  Google Scholar 

  • Wu, C., and Gilbert, W., 1981, Tissue-specific exposure of chromatin structure at the 5’ terminus of the rat preproinsulin II gene, Proc. Natl. Acad. Sci. U.S.A. 78: 1577–1580.

    Article  PubMed  CAS  Google Scholar 

  • Wu, C., Bingham, P. M., Livak, K. J., Holmgren, R., and Elgin, S. C. R., 1979a, The chromatin structure of specific genes. I. Evidence for higher order domains of defined DNA sequence, Cell 16: 797–806.

    Article  PubMed  CAS  Google Scholar 

  • Wu, C., Wong, Y.-C., and Elgin, S. C. R., 1979b, The chromatin structure of specific genes. II. Disruption of chromatin structure during gene activity, Cell 16: 807–814.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1984 Plenum Press, New York

About this chapter

Cite this chapter

Keene, M.A., Cartwright, I.L., Fleischmann, G., Lowenhaupt, K., Steiner, E., Elgin, S.C.R. (1984). Some Observations on DNA Structure and Chromatin Organization at Specific Loci in Drosophila melanogaster . In: Kumar, A. (eds) Eukaryotic Gene Expression. GWUMC Department of Biochemistry Annual Spring Symposia. Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-7459-6_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-4684-7459-6_1

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4684-7461-9

  • Online ISBN: 978-1-4684-7459-6

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics