Skip to main content
PMC home page
Genetics logoLink to Genetics
. 2001 Dec;159(4):1649–1658. doi: 10.1093/genetics/159.4.1649

The gypsy insulator of Drosophila affects chromatin structure in a directional manner.

S Chen 1, V G Corces 1
PMCID: PMC1461898  PMID: 11779804

Abstract

Chromatin insulators are thought to regulate gene expression by establishing higher-order domains of chromatin organization, although the specific mechanisms by which these sequences affect enhancer-promoter interactions are not well understood. Here we show that the gypsy insulator of Drosophila can affect chromatin structure. The insulator itself contains several DNase I hypersensitive sites whose occurrence is dependent on the binding of the Suppressor of Hairy-wing [Su(Hw)] protein. The presence of the insulator in the 5' region of the yellow gene increases the accessibility of the DNA to nucleases in the promoter-proximal, but not the promoter-distal, region. This increase in accessibility is not due to alterations in the primary chromatin fiber, because the number and position of the nucleosomes appears to be the same in the presence or absence of the insulator. Binding of the Su(Hw) protein to insulator DNA is not sufficient to induce changes in chromatin accessibility, and two domains of this protein, presumed to be involved in interactions with other insulator components, are essential for this effect. The presence of Modifier of mdg4 [Mod(mdg4)] protein, a second component of the gypsy insulator, is required to induce these alterations in chromatin accessibility. The results suggest that the gypsy insulator affects chromatin structure and offer insights into the mechanisms by which insulators affect enhancer-promoter interactions.

Full Text

The Full Text of this article is available as a PDF (342.2 KB).

Selected References

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

  1. Cai H., Levine M. Modulation of enhancer-promoter interactions by insulators in the Drosophila embryo. Nature. 1995 Aug 10;376(6540):533–536. doi: 10.1038/376533a0. [DOI] [PubMed] [Google Scholar]
  2. Cavalli G., Paro R. Chromo-domain proteins: linking chromatin structure to epigenetic regulation. Curr Opin Cell Biol. 1998 Jun;10(3):354–360. doi: 10.1016/s0955-0674(98)80011-2. [DOI] [PubMed] [Google Scholar]
  3. De Boni U. The interphase nucleus as a dynamic structure. Int Rev Cytol. 1994;150:149–171. doi: 10.1016/s0074-7696(08)61541-7. [DOI] [PubMed] [Google Scholar]
  4. Dorn R., Krauss V., Reuter G., Saumweber H. The enhancer of position-effect variegation of Drosophila, E(var)3-93D, codes for a chromatin protein containing a conserved domain common to several transcriptional regulators. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):11376–11380. doi: 10.1073/pnas.90.23.11376. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dorsett D. Distant liaisons: long-range enhancer-promoter interactions in Drosophila. Curr Opin Genet Dev. 1999 Oct;9(5):505–514. doi: 10.1016/s0959-437x(99)00002-7. [DOI] [PubMed] [Google Scholar]
  6. Gasser S. M., Laemmli U. K. Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell. 1986 Aug 15;46(4):521–530. doi: 10.1016/0092-8674(86)90877-9. [DOI] [PubMed] [Google Scholar]
  7. Gause M., Morcillo P., Dorsett D. Insulation of enhancer-promoter communication by a gypsy transposon insert in the Drosophila cut gene: cooperation between suppressor of hairy-wing and modifier of mdg4 proteins. Mol Cell Biol. 2001 Jul;21(14):4807–4817. doi: 10.1128/MCB.21.14.4807-4817.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gdula D. A., Corces V. G. Characterization of functional domains of the su(Hw) protein that mediate the silencing effect of mod(mdg4) mutations. Genetics. 1997 Jan;145(1):153–161. doi: 10.1093/genetics/145.1.153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gerasimova T. I., Byrd K., Corces V. G. A chromatin insulator determines the nuclear localization of DNA. Mol Cell. 2000 Nov;6(5):1025–1035. doi: 10.1016/s1097-2765(00)00101-5. [DOI] [PubMed] [Google Scholar]
  10. Gerasimova T. I., Corces V. G. Polycomb and trithorax group proteins mediate the function of a chromatin insulator. Cell. 1998 Feb 20;92(4):511–521. doi: 10.1016/s0092-8674(00)80944-7. [DOI] [PubMed] [Google Scholar]
  11. Gerasimova T. I., Gdula D. A., Gerasimov D. V., Simonova O., Corces V. G. A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation. Cell. 1995 Aug 25;82(4):587–597. doi: 10.1016/0092-8674(95)90031-4. [DOI] [PubMed] [Google Scholar]
  12. Geyer P. K., Corces V. G. DNA position-specific repression of transcription by a Drosophila zinc finger protein. Genes Dev. 1992 Oct;6(10):1865–1873. doi: 10.1101/gad.6.10.1865. [DOI] [PubMed] [Google Scholar]
  13. Geyer P. K., Spana C., Corces V. G. On the molecular mechanism of gypsy-induced mutations at the yellow locus of Drosophila melanogaster. EMBO J. 1986 Oct;5(10):2657–2662. doi: 10.1002/j.1460-2075.1986.tb04548.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Geyer P. K. The role of insulator elements in defining domains of gene expression. Curr Opin Genet Dev. 1997 Apr;7(2):242–248. doi: 10.1016/s0959-437x(97)80134-7. [DOI] [PubMed] [Google Scholar]
  15. Ghosh D., Gerasimova T. I., Corces V. G. Interactions between the Su(Hw) and Mod(mdg4) proteins required for gypsy insulator function. EMBO J. 2001 May 15;20(10):2518–2527. doi: 10.1093/emboj/20.10.2518. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Harrison D. A., Gdula D. A., Coyne R. S., Corces V. G. A leucine zipper domain of the suppressor of Hairy-wing protein mediates its repressive effect on enhancer function. Genes Dev. 1993 Oct;7(10):1966–1978. doi: 10.1101/gad.7.10.1966. [DOI] [PubMed] [Google Scholar]
  17. Hebbes T. R., Allen S. C. Multiple histone acetyltransferases are associated with a chicken erythrocyte chromatin fraction enriched in active genes. J Biol Chem. 2000 Oct 6;275(40):31347–31352. doi: 10.1074/jbc.M004830200. [DOI] [PubMed] [Google Scholar]
  18. Holdridge C., Dorsett D. Repression of hsp70 heat shock gene transcription by the suppressor of hairy-wing protein of Drosophila melanogaster. Mol Cell Biol. 1991 Apr;11(4):1894–1900. doi: 10.1128/mcb.11.4.1894. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kellum R., Schedl P. A group of scs elements function as domain boundaries in an enhancer-blocking assay. Mol Cell Biol. 1992 May;12(5):2424–2431. doi: 10.1128/mcb.12.5.2424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kellum R., Schedl P. A position-effect assay for boundaries of higher order chromosomal domains. Cell. 1991 Mar 8;64(5):941–950. doi: 10.1016/0092-8674(91)90318-s. [DOI] [PubMed] [Google Scholar]
  21. Lamond A. I., Earnshaw W. C. Structure and function in the nucleus. Science. 1998 Apr 24;280(5363):547–553. doi: 10.1126/science.280.5363.547. [DOI] [PubMed] [Google Scholar]
  22. Lu Q., Wallrath L. L., Granok H., Elgin S. C. (CT)n (GA)n repeats and heat shock elements have distinct roles in chromatin structure and transcriptional activation of the Drosophila hsp26 gene. Mol Cell Biol. 1993 May;13(5):2802–2814. doi: 10.1128/mcb.13.5.2802. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Manuelidis L., Chen T. L. A unified model of eukaryotic chromosomes. Cytometry. 1990;11(1):8–25. doi: 10.1002/cyto.990110104. [DOI] [PubMed] [Google Scholar]
  24. Mirkovitch J., Mirault M. E., Laemmli U. K. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell. 1984 Nov;39(1):223–232. doi: 10.1016/0092-8674(84)90208-3. [DOI] [PubMed] [Google Scholar]
  25. Prioleau M. N., Nony P., Simpson M., Felsenfeld G. An insulator element and condensed chromatin region separate the chicken beta-globin locus from an independently regulated erythroid-specific folate receptor gene. EMBO J. 1999 Jul 15;18(14):4035–4048. doi: 10.1093/emboj/18.14.4035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Roseman R. R., Swan J. M., Geyer P. K. A Drosophila insulator protein facilitates dosage compensation of the X chromosome min-white gene located at autosomal insertion sites. Development. 1995 Nov;121(11):3573–3582. doi: 10.1242/dev.121.11.3573. [DOI] [PubMed] [Google Scholar]
  27. Saitoh N., Bell A. C., Recillas-Targa F., West A. G., Simpson M., Pikaart M., Felsenfeld G. Structural and functional conservation at the boundaries of the chicken beta-globin domain. EMBO J. 2000 May 15;19(10):2315–2322. doi: 10.1093/emboj/19.10.2315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Scott K. S., Geyer P. K. Effects of the su(Hw) insulator protein on the expression of the divergently transcribed Drosophila yolk protein genes. EMBO J. 1995 Dec 15;14(24):6258–6267. doi: 10.1002/j.1460-2075.1995.tb00316.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Sudarsanam P., Winston F. The Swi/Snf family nucleosome-remodeling complexes and transcriptional control. Trends Genet. 2000 Aug;16(8):345–351. doi: 10.1016/s0168-9525(00)02060-6. [DOI] [PubMed] [Google Scholar]
  30. Udvardy A., Maine E., Schedl P. The 87A7 chromomere. Identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains. J Mol Biol. 1985 Sep 20;185(2):341–358. doi: 10.1016/0022-2836(85)90408-5. [DOI] [PubMed] [Google Scholar]
  31. Wallrath L. L., Elgin S. C. Position effect variegation in Drosophila is associated with an altered chromatin structure. Genes Dev. 1995 May 15;9(10):1263–1277. doi: 10.1101/gad.9.10.1263. [DOI] [PubMed] [Google Scholar]
  32. Yokota H., van den Engh G., Hearst J. E., Sachs R. K., Trask B. J. Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus. J Cell Biol. 1995 Sep;130(6):1239–1249. doi: 10.1083/jcb.130.6.1239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Zhao K., Hart C. M., Laemmli U. K. Visualization of chromosomal domains with boundary element-associated factor BEAF-32. Cell. 1995 Jun 16;81(6):879–889. doi: 10.1016/0092-8674(95)90008-x. [DOI] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES