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


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.

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Data availability

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


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


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.

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Correspondence to Igor F. Zhimulev.

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Supplementary Fig 1.

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)

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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

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