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Global chromatin conformation differences in the Drosophila dosage compensated chromosome X

Author

Listed:
  • Koustav Pal

    (IFOM, the FIRC Institute of Molecular Oncology)

  • Mattia Forcato

    (University of Modena and Reggio Emilia)

  • Daniel Jost

    (University of Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG
    University of Lyon, ENS de Lyon, University of Claude Bernard, CNRS UMR 5239)

  • Thomas Sexton

    (IGH, Institute of Human Genetics, CNRS UPR1142
    Institute of Genetics and Molecular and Cellular Biology (IGBMC))

  • Cédric Vaillant

    (University of Lyon, ENS de Lyon, University of Claude Bernard, CNRS, Laboratoire de Physique)

  • Elisa Salviato

    (IFOM, the FIRC Institute of Molecular Oncology)

  • Emilia Maria Cristina Mazza

    (Humanitas Clinical and Research Center)

  • Enrico Lugli

    (Humanitas Clinical and Research Center)

  • Giacomo Cavalli

    (IGH, Institute of Human Genetics, CNRS UPR1142)

  • Francesco Ferrari

    (IFOM, the FIRC Institute of Molecular Oncology
    Institute of Molecular Genetics, National Research Council)

Abstract

In Drosophila melanogaster the single male chromosome X undergoes an average twofold transcriptional upregulation for balancing the transcriptional output between sexes. Previous literature hypothesised that a global change in chromosome structure may accompany this process. However, recent studies based on Hi-C failed to detect these differences. Here we show that global conformational differences are specifically present in the male chromosome X and detectable using Hi-C data on sex-sorted embryos, as well as male and female cell lines, by leveraging custom data analysis solutions. We find the male chromosome X has more mid-/long-range interactions. We also identify differences at structural domain boundaries containing BEAF-32 in conjunction with CP190 or Chromator. Weakening of these domain boundaries in male chromosome X co-localizes with the binding of the dosage compensation complex and its co-factor CLAMP, reported to enhance chromatin accessibility. Together, our data strongly indicate that chromosome X dosage compensation affects global chromosome structure.

Suggested Citation

  • Koustav Pal & Mattia Forcato & Daniel Jost & Thomas Sexton & Cédric Vaillant & Elisa Salviato & Emilia Maria Cristina Mazza & Enrico Lugli & Giacomo Cavalli & Francesco Ferrari, 2019. "Global chromatin conformation differences in the Drosophila dosage compensated chromosome X," Nature Communications, Nature, vol. 10(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13350-8
    DOI: 10.1038/s41467-019-13350-8
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    Cited by:

    1. Mujahid Ali & Lubna Younas & Jing Liu & Huangyi He & Xinpei Zhang & Qi Zhou, 2024. "Development and evolution of Drosophila chromatin landscape in a 3D genome context," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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