Polytene chromosomes reflect functional organization of the Drosophila genome

Polytene chromosomes of Drosophila melanogaster are a convenient model for studying interphase chromosomes of eukaryotes. They are giant in size in comparison with diploid cell chromosomes and have a pattern of cross stripes resulting from the ordered chromatid arrangement. Each region of polytene chromosomes has a unique banding pattern. Using the model of four chromatin types that reveals domains of varying compaction degrees, we were able to correlate the physical and cytological maps of some polytene chromosome regions and to show the main properties of genetic and molecular organization of bands and interbands, that we describe in this review. On the molecular map of the genome, the interbands correspond to decompacted aquamarine chromatin and 5’ ends of ubiquitously active genes. Gray bands contain lazurite and malachite chromatin, intermediate in the level of compaction, and, mainly, coding parts of genes. Dense black transcriptionally inactive bands are enriched in ruby chromatin. Localization of several dozens of interbands on the genome molecular map allowed us to study in detail their architecture according to the data of whole genome projects. The distribution of proteins and regulatory elements of the genome in the promoter regions of genes localized in the interbands shows that these parts of interbands are probably responsible for the formation of open chromatin that is visualized in polytene chromosomes as interbands. Thus, the permanent genetic activity of interbands and gray bands and the inactivity of genes in black bands are the basis of the universal banding pattern in the chromosomes of all Drosophila tissues. The smallest fourth chromosome of Drosophila with an atypical protein composition of chromatin is a special case.  Using the model of four chromatin states and fluorescent in situ hybridization, its cytological map was refined and the genomic coordinates of all bands and interbands were determined. It was shown that, in spite of the peculiarities of this chromosome, its band organization in general corresponds to the rest of the genome. Extremely long genes of different Drosophila chromosomes do not fit the common scheme, since they can occupy a series of alternating bands and interbands (up to nine chromosomal structures) formed by parts of these genes.

Drosophila melanogaster, polytene chromosomes, interphase chromosomes, four chromatin state model, fluorescent in situ hybridization, genetic organization, bands and interbands of chromosomes

1. Andreyeva E.N., Kolesnikova T.D., Demakova O.V., Mendez-Lago M., Pokholkova G.V., Belyaeva E.S., Rossi F., Dimitri P., Villasante A., Zhimulev I.F. High-resolution analysis of Drosophila heterochroma¬tin organization using SuUR Su(var)3-9 double mutants. Proc. Natl. Acad. Sci USA. 2007;104(31):12819-12824.

2. Boldyreva L.V., Goncharov F.P., Demakova O.V., Zykova T.Y., Levit¬sky V.G., Kolesnikov N.N., Pindyurin A.V., Semeshin V.F., Zhimu- lev I.F. Protein and genetic composition of four chromatin types in Drosophila melanogaster cell lines. Curr. Genomics. 2017;18(2): 214-226.

3. Bridges C.B. Cytological data on chromosome four of Drosophila me- lanogaster. Trans. Dyn. Dev. 1935;10:463-473.

4. Czermin B., Melfi R., McCabe D., Seitz V., Imhof A., Pirrotta V. Dro-sophila enhancer of Zeste/ESC complexes have a histone H3 me- thyltransferase activity that marks chromosomal Polycomb sites. Cell. 2002;111(2):185-196.

5. Demakov S.A., Semeshin V.F., Zhimulev I.F. Cloning and molecular genetic analysis of Drosophila melanogaster interband DNA. Mol. Gen. Genet. 1993;238(3):437-443.

6. Demakov S.A., Vatolina T.Y., Babenko V.N., Semeshin V.F., Belyae-va E.S., Zhimulev I.F. Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster. BMC Genomics. 2011;12(1):566.

7. Demakova O.V., Pokholkova G.V., Kolesnikova T.D., Demakov S.A., Andreyeva E.N., Belyaeva E.S., Zhimulev I.F. The SU(VAR)3-9/ HP1 complex differentially regulates the compaction state and de¬gree of underreplication of X chromosome pericentric heterochro¬matin in Drosophila melanogaster. Genetics. 2007;175(2):609-620.

8. Eaton M.L., Prinz J.A., MacAlpine H.K., Tretyakov G., Kharchen¬ko P.V., MacAlpine D.M. Chromatin signatures of the Drosophila replication program. Genome Res. 2011;21(2):164-174.

9. Figueiredo M.L., Philip P., Stenberg P., Larsson J. HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila mela¬nogaster. PLoS Genet. 2012;8(11):e1003061.

10. Hoskins R.A., Landolin J.M., Brown J.B., Sandler J.E., Takahashi H., Lassmann T., Yu C., Booth B.W., Zhang D., Wan K.H., Yang L., Boley N., Andrews J., Kaufman T.C., Graveley B.R., Bickel P.J., Carninci P., Carlson J.W., Celniker S.E. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011;21(2):182-192.

11. James T.C., Eissenberg J.C., Craig C., Dietrich V., Hobson A., El¬gin S.C. Distribution patterns of HP1, a heterochromatin-associated nonhistone chromosomal protein of Drosophila. Eur. J. Cell Biol. 1989;50(1):170-180.

12. Johansson A.M., Stenberg P., Bernhardsson C., Larsson J. Painting of fourth and chromosome-wide regulation of the 4th chromosome in Drosophila melanogaster. EMBO J. 2007a;26(9):2307-2316.

13. Johansson A.M., Stenberg P., Pettersson F., Larsson J. POF and HP1 bind expressed exons, suggesting a balancing mechanism for gene regulation. PLoS Genet. 2007b;3(11):e209.

14. Kharchenko P.V., Alekseyenko A.A., Schwartz Y.B., Minoda A., Rid-dle N.C., Ernst J., Sabo P.J., Larschan E., Gorchakov A.A., Gu T., Linder-Basso D., Plachetka A., Shanower G., Tolstorukov M.Y., Lu- quette L.J., Xi R., Jung Y.L., Park R.W., Bishop E.P., Canfield T.K., Sandstrom R., Thurman R.E., MacAlpine D.M., Stamatoyannopou- los J.A., Kellis M., Elgin S.C., Kuroda M.I., Pirrotta V., Karpen G.H., Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011;471(7339):480-485.

15. Kholodilov N.G., Bolshakov V.N., Blinov V.M., Solovyov V.V., Zhimu¬lev I.F. Intercalary heterochromatin in Drosophila. III. Homology between DNA sequences from the Y chromosome, bases of polytene chromosome limbs, and chromosome 4 of D. melanogaster. Chro¬mosoma. 1988;97(3):247-253.

16. Khoroshko V.A., Levitsky V.G., Zykova T.Y., Antonenko O.V., Belyae¬va E.S., Zhimulev I.F. Chromatin heterogeneity and distribution of regulatory elements in the late-replicating intercalary heterochroma¬tin domains of Drosophila melanogaster chromosomes. PLoS One. 2016;11(6):e0157147.

17. Khoroshko V.A., Pokholkova G.V., Zykova T.Yu., Osadchiy I.S., Zhi¬mulev I.F. Gene dunce localization in the polytene chromosome of Drosophila melanogaster long span batch of adjacent chromosomal structures. Dokl. Biochem. Biophys. 2019;484(4):1-4.

18. Khoroshko V.A., Zykova T.Yu., Popova O.O., Zhimulev I.F. Border structure of intercalary heterochromatin bands of Drosophila me- lanogaster polytene chromosomes. Dokl. Biochem. Biophys. 2018; 479(1):114-117.

19. Kim M., Ekhteraei-Tousi S., Lewerentz J., Larsson J. The X-linked 1.688 satellite in Drosophila melanogaster promotes specific target¬ing by painting of fourth. Genetics. 2018;208(2):623-632.

20. Kolesnikova T.D., Goncharov F.P., Zhimulev I.F. Similarity in replica¬tion timing between polytene and diploid cells is associated with the organization of the Drosophila genome. PLoS One. 2018;13(4): e0195207.

21. Larsson J., Chen J.D., Rasheva V, Rasmuson-Lestander A., Pirrotta V. Painting of fourth, a chromosome-specific protein in Drosophila. Proc. Natl. Acad. Sci. USA. 2001;98(11):6273-6278.

22. Larsson J., Svensson M.J., Stenberg P., Makitalo M. Painting of fourth in genus Drosophila suggests autosome-specific gene regulation. Proc. Natl. Acad. Sci. USA. 2004;101(26):9728-9733.

23. Lundberg L.E., Kim M., Johansson A.M., Faucillion M.L., Josupeit R., Larsson J. Targeting of Painting of fourth to roX1 and roX2 proxi¬mal sites suggests evolutionary links between dosage compensation and the regulation of the fourth chromosome in Drosophila melano- gaster. G3 (Bethesda). 2013;3(8):1325-1334.

24. modENCODE consortium, Roy S., Ernst J., Kharchenko P.V., Kherad- pour P., Negre N., Eaton M.L., Landolin J.M., Bristow C.A., Ma L., Lin M.F., Washietl S., Arshinoff B.I., Ay F., Meyer P.E., Robine N., Washington N.L., Di Stefano L., Berezikov E., Brown C.D., Can- deias R., Carlson J.W., Carr A., Jungreis I., Marbach D., Seal- fon R., Tolstorukov M.Y., Will S., Alekseyenko A.A., Artieri C., Booth B.W., Brooks A.N., Dai Q., Davis C.A., Duff M.O., Feng X., Gorchakov A.A., Gu T., Henikoff J.G., Kapranov P, Li R., MacAl¬pine H.K., Malone J., Minoda A., Nordman J., Okamura K., Perry M., Powell S.K., Riddle N.C., Sakai A., Samsonova A., Sandler J.E., Schwartz Y.B., Sher N., Spokony R., Sturgill D., van Baren M., Wan K.H., Yang L., Yu C., Feingold E., Good P., Guyer M., Low- don R., Ahmad K., Andrews J., Berger B., Brenner S.E., Brent M.R., Cherbas L., Elgin S.C., Gingeras T.R., Grossman R., Hoskins R.A., Kaufman T.C., Kent W., Kuroda M.I., Orr-Weaver T., Perrimon N., Pirrotta V, Posakony J.W., Ren B., Russell S., Cherbas P, Grave- ley B.R., Lewis S., Micklem G., Oliver B., Park P.J., Celniker S.E., Henikoff S., Karpen G.H., Lai E.C., MacAlpine D.M., Stein L.D., White K.P., Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010; 330(6012):1787-1797.

25. Nechaev S., Fargo D.C., dos Santos G., Liu L., Gao Y., Adelman K. Global analysis of short RNAs reveals widespread promoter-proxi¬mal stalling and arrest of Pol II in Drosophila. Science. 2010; 327(5963):335-338.

26. Riddle N.C., Elgin S.C. The dot chromosome of Drosophila: insights into chromatin states and their change over evolutionary time. Chro¬mosome Res. 2006;14(4):405-416.

27. Riddle N.C., Shaffer C.D., Elgin S.C. A lot about a little dot - lessons learned from Drosophila melanogaster chromosome 4. Biochem. Cell. Biol. 2009;87(1):229-241.

28. Semeshin V.F., Demakov S.A., Shloma V.V., Vatolina T.Y., Gorcha-kov A.A., Zhimulev I.F. Interbands behave as decompacted autono¬mous units in Drosophila melanogaster polytene chromosomes. Ge- netica. 2008;132(3):267-279.

29. Seum C., Reo E., Peng H., Rauscher F.J., Spierer P, Bontron S. Dro-sophila SETDB1 is required for chromosome 4 silencing. PLoS Genet. 2007;3(5):e76.

30. Sher N., Bell G.W., Li S., Nordman J., Eng T., Eaton M.L., MacAl¬pine D.M., Orr-Weaver T.L. Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res. 2012;22(1):64-75.

31. Sidorenko D.S., Sidorenko I.A., Zykova T.Yu., Kolesnikova T.D., Goncharov F.P., Zhimulev I.F. Molecular and genetic organization of bands and interbands in the dot chromosome of Drosophila me- lanogaster. Chromosome 2018: International Conference. August 20-24, 2018, Novosibirsk, Russia. Abstracts. Novosibirsk: Institute of Molecular and Cellular Biology SB RAS; Novosibirsk State Uni¬versity, 2018;75.

32. Slawson E.E., Shaffer C.D., Malone C.D., Leung W., Kellmann E., Shevchek R.B., Craig C.A., Bloom S.M., Bogenpohl J., Dee J., Morimoto E.T., Myoung J., Nett A.S., Ozsolak F., Tittiger M.E., Zeug A., Pardue M.L., Buhler J., Mardis E.R., Elgin S.C. Com-parison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biol. 2006;7(2):R15.

33. Vatolina T.Yu., Boldyreva L.V., Demakova O.V., Demakov S.A., Ko- koza E.B., Semeshin V.F., Babenko V.N., Goncharov F.P., Belyae-va E.S., Zhimulev I.F. Identical functional organization of nonpoly- tene and polytene chromosomes in Drosophila melanogaster. PLoS One. 2011a;6(10):e25960.

34. Vatolina T.Iu., Demakov S.A., Semeshin V.F., Makunin I.V., Baben-ko V.N., Beliaeva E.S., Zhimulev I.F. Identification and molecular genetic characterization of the polytene chromosome interbands in Drosophila melanogaster. Russ. J. Genet. 2011b;47(5):521-532.

35. Vogelmann J., Le Gall A., Dejardin S., Allemand F., Gamot A., La- besse G., Cuvier O., Negre N., Cohen-Gonsaud M., Margeat E., Nollmann M. Chromatin insulator factors involved in long-range DNA interactions and their role in the folding of the Drosophila ge¬nome. PLoS Genet. 2014;10(8):e1004544.

36. Zhimulev I.F., Boldyreva L.V., Demakova O.V., Poholkova G.V., Khoroshko V.A., Zykova T.Y., Lavrov S.A., Belyaeva E.S. Dro-sophila polytene chromosome bands formed by gene introns. Dokl. Biochem. Biophys. 2016;466(1):57-60.

37. Zhimulev I.F., Zykova T.Y., Goncharov F.P., Khoroshko V.A., Dema¬kova O.V., Semeshin V.F., Pokholkova G.V., Boldyreva L.V., Demi¬dova D.S., Babenko V.N., Demakov S.A., Belyaeva E.S. Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster. PLoS One. 2014;9(7):e101631.

38. Zykova T.Yu., Levitsky V.G., Belyaeva E.S., Zhimulev I.F. Polytene chromosomes - a portrait of functional organization of the Droso-phila genome. Curr. Genomics. 2018;19(3):179-191.

39. Zykova T.Yu., Levitsky V.G., Zhimulev I.F. Architecture of promoters of house-keeping genes in polytene chromosome interbands of Dro¬sophila melanogaster. Dokl. Biochem. Biophys. 2019;485(1):1-6.