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Doklady Biochemistry and Biophysics

, Volume 485, Issue 1, pp 95–100 | Cite as

Architecture of Promoters of House-Keeping Genes in Polytene Chromosome Interbands of Drosophila melanogaster

  • T. Yu. ZykovaEmail author
  • V. G. Levitsky
  • I. F. Zhimulev
BIOCHEMISTRY, BIOPHYSICS, AND MOLECULAR BIOLOGY

Abstract

This is the first study to investigate the molecular-genetic organization of polytene chromosome interbands located on both molecular and cytological maps of Drosophila genome. The majority of the studied interbands contained one gene with a single transcription initiation site; the remaining interbands contained one gene with several alternative promoters, two or more unidirectional genes, and “head-to-head” arranged genes. In addition, intricately arranged interbands containing three or more genes in both unidirectional and bidirectional orientation were found. Insulator proteins, ORC, P-insertions, DNase I hypersensitive sites, and other open chromatin structures were situated in the promoter region of the genes located in the interbands. This area is critical for the formation of the interband, an open chromatin region in which gene transcription and replication are combined.

Notes

REFERENCES

  1. 1.
    Kharchenko, P.V., Alekseyenko, A.A., Schwartz, Y.B., et al., Comprehensive analysis of the chromatin landscape in Drosophila melanogaster, Nature, 2011, vol. 471, no. 7339, pp. 480–485.CrossRefGoogle Scholar
  2. 2.
    Zhimulev, I.F., Zykova, T.Y., Goncharov, F.P., Khoroshko, V.A., Demakova, O.V., Semeshin, V.F., Po-kholkova, G.V., Boldyreva, L.V., Demidova, D.S., Babenko, V.N., Demakov, S.A., and Belyaeva, E.S., Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster, PLoS One, 2014, vol. 9, no. 7. e101631.CrossRefGoogle Scholar
  3. 3.
    Zhimulev, I., Belyaeva, E., Makunin, I., Pirrotta, V., Volkova, E., and Alekseyenko, A., Influence of the suur gene on intercalary heterochromatin in Drosophila melanogaster polytene chromosomes, Chromosoma, 2003, vol. 111, no. 6, pp. 377–398.CrossRefGoogle Scholar
  4. 4.
    Vatolina, T.Yu., Boldyreva, L.V., Demakova, O.V., Demakov, S.A., Kokoza, E.B., Semeshin, V.F., Babenko, V.N., Goncharov, F.P., Belyaeva, E.S., and Zhimulev, I.F., Identical functional organization of cell line interphase and polytene chromosomes in Droso-phila melanogaster, PLoS One, 2011, vol. 6, no. 10. e25960.CrossRefGoogle Scholar
  5. 5.
    Khoroshko, V.A., Levitsky, V.G., Zykova, T.Y., Antonenko, O.V., Belyaeva, E.S., and Zhimulev, I.F., Chromatin heterogeneity and distribution of regulatory elements in the late-replicating intercalary heterochromatin domains of Drosophila melanogaster chromosomes, PLoS One, 2016, vol. 11, no. 6. e0157147.CrossRefGoogle Scholar
  6. 6.
    Zhimulev, I.F., Belyaeva, E.S., Semeshin, V.F., Koryakov, D.E., Demakov, S.A., Demakova, O.V., Pokholkova, G.V., and Andreyeva, E.N., Polytene chromosomes: 70 years of genetic research, Int. Rev. Cytol., 2004, vol. 241, pp. 203–275.CrossRefGoogle Scholar
  7. 7.
    Beermann, W., Chromomeres and genes, Results Probl. Cell Diff., 1972, vol. 4, pp. 1–33.CrossRefGoogle Scholar
  8. 8.
    Zykova, T., Popova, O., Khoroshko, V., Levitskii, V., Lavrov, S., and Zhimulev, I. Genetic organization of open chromatin domains situated in polytene chromosome interbands in Drosophila, Dokl. Biochem. Biophys., 2018, vol. 483, pp. 297–301.CrossRefGoogle Scholar
  9. 9.
    Zykova, T., Levitsky, V., Belyaeva, E., and Zhimulev, I., Polytene chromosomes—a portrait of functional organization of the Drosophila genome, Curr. Genomics, 2018, vol. 19, no. 3, pp. 179–191.CrossRefGoogle Scholar
  10. 10.
    Pokholkova, G., Demakov, S., Andreenkov, O., Andreenkova, N., Volkova, E., Belyaeva, E., and Zhimulev, I., Tethering of CHROMATOR and dCTCF proteins results in decompaction of condensed bands in the Drosophila melanogaster polytene chromosomes but does not affect their transcription and replication timing, PLoS One, 2018, vol. 13, no. 4. e0192634.CrossRefGoogle Scholar
  11. 11.
    Vogelmann, J., Le Gall, A., Dejardin, S., Allemand, F., Gamot, A., Labesse, G., Cuvier, O., Nègre, N., Cohen-Gonsaud, M., Margeat, E., and Nöllmann, M., Chromatin insulator factors involved in long-range DNA interactions and their role in the folding of the Drosophila genome, PLoS Genet., 2014, vol. 10, no. 8. e1004544.CrossRefGoogle Scholar
  12. 12.
    Henriques, T., Gilchrist, D., Nechaev, S., Bern, M., Muse, G., Burkholder, A., Fargo, D., and Adelman, K., Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals, Mol. Cell, 2013, vol. 52, no. 4, pp. 517–528.CrossRefGoogle Scholar
  13. 13.
    Nechaev, S., Fargo, D., Santos, G., Liu, L., Gao, Y., and Adelman, K., Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila, Science, 2010, vol. 327, no. 5963, pp. 335–338.CrossRefGoogle Scholar
  14. 14.
    Eaton, M.L., Prinz, J.A., MacAlpine, H.K., Tretyakov, G., Kharchenko, P.V., and MacAlpine, D.M., Chromatin signatures of the Drosophila replication program, Genome Res., 2011, vol. 21, no. 2, pp. 164–174.CrossRefGoogle Scholar
  15. 15.
    Hoskins, R.A., Landolin, J.M., Brown, J.B., Sandler, J.E., Takahashi, H., et al., Genome-wide analysis of promoter architecture in Drosophila melanogaster, Genome Res., 2011, vol. 21, no. 2, pp. 182–192.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2019

Authors and Affiliations

  • T. Yu. Zykova
    • 1
    Email author
  • V. G. Levitsky
    • 2
    • 3
  • I. F. Zhimulev
    • 1
    • 3
  1. 1.Institute of Molecular and Cellular Biology, Siberian Branch, Russian Academy of SciencesNovosibirskRussia
  2. 2.Institute of Cytology and Genetics, Siberian Branch, Russian Academy of SciencesNovosibirskRussia
  3. 3.Novosibirsk State UniversityNovosibirskRussia

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