Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes

Abstract

In Drosophila melanogaster, the chromatin of interphase polytene chromosomes appears as alternating decondensed interbands and dense black or thin gray bands. Recently, we uncovered four principle chromatin states (4НММ model) in the fruit fly, and these were matched to the structures observed in polytene chromosomes. Ruby/malachite chromatin states form black bands containing developmental genes, whereas aquamarine chromatin corresponds to interbands enriched with 5′ regions of ubiquitously expressed genes. Lazurite chromatin supposedly forms faint gray bands and encompasses the bodies of housekeeping genes. In this report, we test this idea using the X chromosome as the model and MSL1 as a protein marker of the lazurite chromatin. Our bioinformatic analysis indicates that in the X chromosome, it is only the lazurite chromatin that is simultaneously enriched for the proteins and histone marks associated with exons, transcription elongation, and dosage compensation. As a result of FISH and EM mapping of a dosage compensation complex subunit, MSL1, we for the first time provide direct evidence that lazurite chromatin forms faint gray bands. Our analysis proves that overall most of housekeeping genes typically span from the interbands (5′ region of the gene) to the gray band (gene body). More rarely, active lazurite chromatin and inactive malachite/ruby chromatin may be found within a common band, where both the housekeeping and the developmental genes reside together.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10
Fig. 11
Fig. 12
Fig. 13

Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

References

  1. Alekseyenko AA, Larschan E, Lai WR, Park PJ, Kuroda MI (2006) High-resolution ChIP–chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev 20:848–857

  2. Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK et al (2008) A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134:599–609

  3. Ashburner M, Golic KG, Hawley RS (2005) Drosophila: a laboratory handbook, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

  4. Belyaeva ES, Zhimulev IF, Volkova EI, Alekseyenko AA, Moshkin YM, Koryakov DE (1998) Su(UR)ES a gene suppressing DNA underreplication in intercalary and pericentric heterochromatin of Drosophila melanogaster polytene chromosomes. Proc Natl Acad Sci U S A 95:7532–7537

  5. Belyaeva ES, Goncharov FP, Demakova OV, Kolesnikova TD, Boldyreva LV, Semeshin VF et al (2012) Late replication domains in polytene and non-polytene cells of Drosophila melanogaster. PLoS One 7:e30035

  6. Belyakin SN, Christophides GK, Alekseyenko AA, Kriventseva EV, Belyaeva ES, Nanayev RA, Makunin IV, Kafatos FC, Zhimulev IF (2005) Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories. Proc Natl Acad Sci U S A 102:8269–8274

  7. Boldyreva LV, Goncharov FP, Demakova OV, Zykova TY, Levitsky VG, Kolesnikov NN, Pindyurin AV, Semeshin VF, Zhimulev IF (2017) Protein and genetic composition of four chromatin types in Drosophila melanogaster. Cell Lines Curr Genom 18:214–226

  8. Braunschweig U, Hogan GJ, Pagie L, van Steensel B (2009) Histone H1 binding is inhibited by histone variant H3.3. EMBO J 28:3635–3645

  9. Bridges CB (1935) Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. J Hered 26:60–64

  10. Bridges CB (1938) A revised map of the salivary gland X-chromosome of Drosophila melanogaster. J Hered 29:11–13

  11. Chlamydas S, Holz H, Samata M, Chelmicki T, Georgiev P, Pelechano V, Dündar F, Dasmeh P, Mittler G, Cadete FT, Ramírez F, Conrad T, Wei W, Raja S, Manke T, Luscombe NM, Steinmetz LM, Akhtar A (2016) Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation. Nat Struct Mol Biol 23(6):580–589. https://doi.org/10.1038/nsmb.3233

  12. Conrad T, Cavalli FM, Holz H, Hallacli E, Kind J, Ilik I, Vaquerizas JM, Luscombe NM, Akhtar A (2012) The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex. Dev Cell 22:610–624

  13. Cugusi S, Kallappagoudar S, Ling H, Lucchesi JC (2015) The Drosophila helicase maleless (MLE) is implicated in functions distinct from its role in dosage compensation. Mol Cell Proteomics 14(6):1478–1488

  14. Demakov SA, Vatolina TY, Babenko VN, Semeshin VF, Belyaeva ES, Zhimulev IF (2011) Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster. BMC Genomics 12:566

  15. Demakova OV, Kotlikova IV, Gordadze PR, Alekseyenko AA, Kuroda MI, Zhimulev IF (2003) The MSL complex levels are critical for its correct targeting to the chromosomes in Drosophila melanogaster. Chromosoma 112:103–115

  16. Demakova OV, Boldyreva LV, Demakov SA, Goncharov FP, Antonenko OV, Zhimulev IF (2016) Characteristic of the chromatin type corresponding to thin “grey” bands in polythene chromosomes of Drosophila melanogaster. Tsitologiya 58:248–252

  17. Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine D (2011) Chromatin signatures of the Drosophila replication program. Genome Res 21(2):164–174

  18. Figueiredo MLA, Kim M, Philip P, Allgardsson A, Stenberg P, Larsson J (2014) Non-coding roX RNAs prevent the binding of the MSL-complex to heterochromatic regions. PLoS Genet 10(12):e1004865. https://doi.org/10.1371/journal.pgen.1004865

  19. Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143:212–224

  20. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80

  21. Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MI (2009) Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes Dev 23:2266–2271

  22. Gortchakov AA, Eggert H, Gan M, Mattow J, Zhimulev IF, Saumweber H (2005) Chriz, a chromodomain protein specific for the interbands of Drosophila melanogaster polytene chromosomes. Chromosoma 114(1):54–66

  23. Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, Bickel PJ, Carninci P, Carlson JW, Celniker SE (2011) Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res 21(2):182–192

  24. Ivaldi MS, Karam CS, Corces VG (2007) Phosphorylation of histone H3 at Ser10 facilitates RNA polymerase II release from promoter-proximal pausing in Drosophila. Genes Dev 21(21):2818–2831

  25. Joshi AA, Struhl K (2005) Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell 20:971–978

  26. Kapoor-Vazirani P, Vertino PM (2014) A dual role for the histone methyltransferase PR-SET7/SETD8 and histone H4 lysine 20 monomethylation in the local regulation of RNA polymerase II pausing. J Biol Chem 289(11):7425–7437

  27. Kelley RL, Solovyeva I, Lyman LM, Richman R, Solovyev V, Kuroda MI (1995) Expression of msl-2 causes assembly of dosage compensation regulators on the X chromosomes and female lethality in Drosophila. Cell 81:867–877

  28. Kelley RL, Wang J, Bell L, Kuroda MI (1997) Sex lethal controls dosage compensation in Drosophila by a non-splicing mechanism. Nature 387(6629):195–199

  29. Kelley RL, Meller VH, Gordadze PR, Roman G, Davis RL, Kuroda MI (1999) Epigenetic spreading of the Drosophila dosage compensation complex from roX RNA genes into flanking chromatin. Cell 98:513–522

  30. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine D, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471:480–485

  31. Khoroshko VA, Levitsky VG, Zykova TY, Antonenko OV, Belyaeva ES, Zhimulev IF (2016) Chromatin heterogeneity and distribution of regulatory elements in the late-replicating intercalary heterochromatin domains of Drosophila melanogaster chromosomes. PLoS One 11:e0157147. https://doi.org/10.1371/journal.pone.0157147

  32. Khoroshko VA, Zykova TY, Popova OO, Zhimulev IF (2018) Border structure of intercalary heterochromatin bands of Drosophila melanogaster polytene chromosomes. Dokl Biochem Biophys 479(1):114–117

  33. Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41:376–381

  34. Kolesnikova TD, Posukh OV, Andreyeva EN, Bebyakina DS, Ivankin AV, Zhimulev IF (2013) Drosophila SUUR protein associates with PCNA and binds chromatin in a cell cycle-dependent manner. Chromosoma 122(1-2):55–66

  35. Kolesnikova TD, Goncharov FP, Zhimulev IF (2018) Similarity in replication timing between polytene and diploid cells is associated with the organization of the Drosophila genome. PLoS One 13:e0195207

  36. Kotlikova IV, Demakova OV, Semeshin VF, Shloma VV, Boldyreva LV, Kuroda MI, Zhimulev IF (2006) The Drosophila dosage compensation complex binds to polytene chromosomes independently of developmental changes in transcription. Genetics 172:963–974

  37. Kozlova TY, Semeshin VF, Tretyakova IV, Kokoza EB, Pirrotta V, Grafodatskaya VE et al (1994) Molecular and cytogenetical characterization of the 10A1-2 band and adjoining region in the Drosophila melanogaster polytene X chromosome. Genetics 136:1063–1073

  38. Kuroda MI, Hilfiker A, Lucchesi JC (2016) Dosage compensation in Drosophila—a model for the coordinate regulation of transcription. Genetics 204(2):435–450

  39. Lam KC, Muhlpfordt F, Vaquerizas JM, Raja SJ, Holz H et al (2012) The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet 8(6):e1002736

  40. Larschan E, Alekseyenko AA, Gorchakov AA, Peng S, Li B et al (2007) MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell 28:121–133

  41. Lawrence M, Gentleman R, Carey V (2009) rtracklayer: an R package for interfacing with genome browsers. Bioinformatics 25:1841–1842

  42. Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ (2013) Software for computing and annotating genomic ranges. PLoS Comput Biol 9:e1003118

  43. Lindsley DL, Zimm GG (1992) The genome of Drosophila melanogaster. Academic Press, San Diego

  44. Lucchesi JC, Kuroda MI (2015) Dosage compensation in Drosophila. Cold Spring Harb Perspect Biol 7(5):a019398. https://doi.org/10.1101/cshperspect.a019398

  45. Milon B, Sun Y, Chang W, Creasy T, Mahurkar A, Shetty A et al (2014) Map of open and closed chromatin domains in Drosophila genome. BMC Genomics 15:988

  46. Nechaev S, Fargo DC, dos Santos G, Liu L, Gao Y, Adelman K (2010) Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila. Science 327(5963):335–338. https://doi.org/10.1126/science.1181421

  47. Philip P, Stenberg P (2013) Male X-linked genes in Drosophila melanogaster are compensated independently of the male-specific lethal complex. Epigenetics Chromatin 6:35

  48. Posukh OV, Maksimov DA, Laktionov PP, Koryakov DE, Belyakin SN (2017) Functional dissection of Drosophila melanogaster SUUR protein influence on H3K27me3 profile. Epigenetics Chromatin 10:56. https://doi.org/10.1186/s13072-017-0163-z

  49. R Development Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna

  50. Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, Akhtar A (2010) The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell 38(6):827–841

  51. Robinson PJ, An W, Routh A, Martino F, Chapman L, Roeder RG, Rhodes D (2008) 30 nm chromatin fibre decompaction requires both H4-K16 acetylation and linker histone eviction. J Mol Biol 381:816–825

  52. Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N et al (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330:1787–1797

  53. Sass GL, Pannuti A, Lucchesi JC (2003) Male-specific lethal complex of Drosophila targets activated regions of the X chromosome for chromatin remodeling. Proc Natl Acad Sci U S A 100:8287–8291

  54. Saura AO, Tapio IH, Sorsa V (1993) Electron microscopic analysis of the banding pattern in the salivary gland chromosomes of Drosophila melanogaster. Divisions 11 through 20 of X. Herediras 119:123–141

  55. Schubeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C et al (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 18:1263–1271

  56. Schwartz S, Meshorer E, Ast G (2009) Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16(9):990–995

  57. Semeshin VF, Zhimulev IF, Belyaeva ES (1979) Electron microscope autoradiographic study on transcriptional activity of Drosophila melanogaster polytene chromosomes. Chromosoma 73:163–177

  58. Semeshin VF, Demakov SA, Alonso PM, Belyaeva ES, Bonner JJ, Zhimulev IF (1989) Electron microscopical analysis of Drosophila polytene chromosomes. Chromosoma 97(5):396–412

  59. Semeshin VF, Artero R, Perez Alonso M, Shloma VV (1998) Electron microscopic in situ hybridization of digoxigenin-dUTP-labelled DNA probes with Drosophila melanogaster polytene chromosomes. Chromosom Res 6:405–410

  60. Semeshin VF, Andreyeva EN, Shloma VV, Saumweber H, Zhimulev IF (2002) Immunogold electron microscope localization of proteins in Drosophila polytene chromosomes: applications and limitations of the method. Chromosom Res 10:429–433

  61. Semeshin VF, Shloma VV, Andreyeva EN, Saumweber H, Zhimulev IF (2003) Use of immunogold labelling technique for immunoelectron microscope localization of proteins in Drosophila polytene chromosomes. Tsitologiya 45(3):235–243

  62. Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL (2012) Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res 22(1):64–75

  63. Shogren-Knaak M, Peterson CL (2006) Switching on chromatin: mechanistic role of histone H4-K16 acetylation. Cell Cycle 5(13):1361–1365

  64. Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G (2012) InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics 28:3163–3165

  65. Steiner LA, Schulz VP, Maksimova Y, Wong C, Gallagher PG (2011) Patterns of histone H3 lysine 27 monomethylation and erythroid cell type-specific gene expression. J Biol Chem 286(45):39457–39465. https://doi.org/10.1074/jbc.M111.243006

  66. Straub T, Becker PB (2008) DNA sequence and the organization of chromosomal domains. Curr Opin Genet Dev 18:175–180

  67. Straub T, Zabel A, Gilfillan GD, Feller C, Becker PB (2013) Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq. Genome Res 23(3):473–485

  68. Vatolina TY, Boldyreva LV, Demakova OV, Demakov SA, Kokoza EB, Semeshin VF et al (2011) Identical functional organization of nonpolytene and polytene chromosomes in Drosophila melanogaster. PLoS One 6:e25960

  69. Wagner EJ, Carpenter PB (2012) Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol 13:115–126

  70. Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, Stark A (2015) Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature 518(7540):556–559

  71. Zeilke T, Glotov A, Saumweber H (2015) High-resolution in situ hybridization analysis on the chromosomal interval 61C7-61C8 of Drosophila melanogaster reveals interbands as open chromatin domains. Chromosoma 125:423–435. https://doi.org/10.1007/s00412-015-0554-5

  72. Zhao K, Hart CM, Laemmli UK (1995) Visualization of chromosomal domains with boundary element-associated factor BEAF-32. Cell 81(6):879–889

  73. Zhimulev IF (1999) Genetic organization of polytene chromosomes. Adv Genet 39:1–589

  74. Zhimulev IF, Semeshin VF, Kulichkov VA, Belyaeva ES (1982) Intercalary heterochromatin in Drosophila. I Localization and general characteristics. Chromosoma 87:197–228

  75. Zhimulev IF, Belyaeva ES, Semeshin VF, Koryakov DE, Demakov SA, Demakova OV, Pokholkova GV, Andreyeva EN (2004) Polytene chromosomes: 70 years of genetic research. Int Rev Cytol 241:203–275

  76. Zhimulev IF, Zykova TY, Goncharov FP, Khoroshko VA, Demakova OV, Semeshin VF et al (2014) Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster. PLoS One 9:e101631

  77. Zykova TY, Levitsky VG, Belyaeva ES, Zhimulev IF (2018) Polytene chromosomes—a portrait of functional organization of the Drosophila genome. Curr Genom 19(3):179–191

Download references

Acknowledgements

We express our deep gratitude to M. Kuroda and R. Kelley for antibodies against MSL1 and transgenic stocks of Drosophila.

Funding

The study was supported by the grant from the Russian Science Foundation (grant number 19-14-00051, bioinformatics analysis), the Fundamental Scientific Research program (0310-2019-0003, immunofluorescence analysis), and the RFBR (grant number 17-00-00284, EM mapping of antibodies and data processing). Data analysis contributed by V.G. Levitsky was supported by the RFBR grant 18-29-13040.

Author information

Correspondence to Igor F. Zhimulev.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Supplementary Fig 1.
figure14

Localization of various protein and genetic features in the region 14B1-2 - 14D1-2 of X chromosome. a Localization of bands within the region 14B1-2 - 14D1-2 of polytene X chromosome according to FlyBase version R 5.57. b Localization of the fragments of marker genes kat80 and para is shown as vertical red and green highlight. с Chromatin states as defined by the chromatin classification models (top-bottom: Zhimulev et al. 2014; Kharchenko et al. 2011 in S2 and BG3 cell lines; Milon et al. 2014; Filion et al. 2010). d Positions of the annotated genes (RefSeq Genes). e Housekeeping and developmental enhancers (Zabidi et al. 2015). f Peak and Broad promoters (Hoskins et al. 2011). g DNAse I Hypersensitive Sites in S2, Kc and BG3 cells (Kharchenko et al. 2011). h Profiles for the ORC2 subunits in the chromosomes from S2, Kc, and BG3 cell lines (Eaton et al. 2011), as well as larval salivary glands (Sher et al. 2012). i Short RNAs derived from stalled RNA polymerase II in Drosophila cells (Nechaev et al. 2010). j Enrichment profiles of NSL complex components: NSL1 binding profile from salivary glands (Raja et al. 2010), NSL3 in S2 cells (Lam et al. 2012). k Transcription initiation-associated histone marks (culture cells, modENCODE data). l Localization of histone H1 dips in Kc cells (Braunschweig et al. 2009). m RNA polymerase II (modENCODE data). n Interband-specific proteins CHRIZ and BEAF (modENCODE data). o MSL1 protein, S2 (modENCODE data). p DCC subunits in wild-type and mutants (Figueiredo et al. 2014). q Gene body-, exon- and transcription elongation-associated histone marks (modENCODE data). r JIL1 protein enrichment across different cell types (modENCODE data). s SUUR distribution in salivary glands obtained by DamID method (Posukh et al. 2017). t SUUR distribution in Kc cells obtained by DamID method (Filion et al. 2010). Blue highlights correspond to grey bands, spaces between the bars correspond to interbands. (PNG 1705 kb)

High Resolution (TIF 91831 kb)

Table S1

(DOCX 22 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Demakova, O.V., Demakov, S.A., Boldyreva, L.V. et al. Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes. Chromosoma 129, 25–44 (2020). https://doi.org/10.1007/s00412-019-00728-2

Download citation

Keywords

  • 4HMM chromatin model
  • Drosophila
  • Polytene chromosome bands and interbands
  • Chromatin types
  • Housekeeping genes
  • MSL1