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Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Author

Listed:
  • Karolina Stępniak

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences)

  • Magdalena A. Machnicka

    (University of Warsaw)

  • Jakub Mieczkowski

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences
    International Research Agenda 3P Medicine Laboratory)

  • Anna Macioszek

    (University of Warsaw)

  • Bartosz Wojtaś

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences)

  • Bartłomiej Gielniewski

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences)

  • Katarzyna Poleszak

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences)

  • Malgorzata Perycz

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences)

  • Sylwia K. Król

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences)

  • Rafał Guzik

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences)

  • Michał J. Dąbrowski

    (Institute of Computer Science of the Polish Academy of Sciences)

  • Michał Dramiński

    (Institute of Computer Science of the Polish Academy of Sciences)

  • Marta Jardanowska

    (Institute of Computer Science of the Polish Academy of Sciences)

  • Ilona Grabowicz

    (Institute of Computer Science of the Polish Academy of Sciences)

  • Agata Dziedzic

    (Institute of Computer Science of the Polish Academy of Sciences)

  • Hanna Kranas

    (University of Warsaw
    The Barcelona Institute of Science and Technology)

  • Karolina Sienkiewicz

    (University of Warsaw)

  • Klev Diamanti

    (Uppsala University)

  • Katarzyna Kotulska

    (The Children’s Memorial Health Institute)

  • Wiesława Grajkowska

    (The Children’s Memorial Health Institute)

  • Marcin Roszkowski

    (The Children’s Memorial Health Institute)

  • Tomasz Czernicki

    (Medical University of Warsaw)

  • Andrzej Marchel

    (Medical University of Warsaw)

  • Jan Komorowski

    (Uppsala University)

  • Bozena Kaminska

    (Nencki Institute of Experimental Biology of the Polish Academy of Sciences)

  • Bartek Wilczyński

    (University of Warsaw)

Abstract

Chromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.

Suggested Citation

  • Karolina Stępniak & Magdalena A. Machnicka & Jakub Mieczkowski & Anna Macioszek & Bartosz Wojtaś & Bartłomiej Gielniewski & Katarzyna Poleszak & Malgorzata Perycz & Sylwia K. Król & Rafał Guzik & Mich, 2021. "Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23922-2
    DOI: 10.1038/s41467-021-23922-2
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