Abstract

Understanding how enhancers drive cell type specificity and efficiently identifying them is essential for the development of innovative therapeutic strategies. In melanoma, the melanocytic (MEL) and the mesenchymal-like (MES) states present themselves with different responses to therapy, making the identification of specific enhancers highly relevant. Using massively parallel reporter assays (MPRA) in a panel of patient-derived melanoma lines (MM lines), we set to identify and decipher melanoma enhancers by first focusing on regions with state specific H3K27 acetylation close to differentially expressed genes. An in-depth evaluation of those regions was then pursued by investigating the activity of overlapping ATAC-seq peaks along with a full tiling of the acetylated regions with 190 bp sequences. Activity was observed in more than 60% of the selected regions and we were able to precisely locate the active enhancers within ATAC-seq peaks. Comparison of sequence content with activity, using the deep learning model DeepMEL2, revealed that AP-1 alone is responsible for the MES enhancer activity. In contrast, SOX10 and MITF both influence MEL enhancer function with SOX10 being required to achieve high levels of activity. Overall, our MPRAs shed light on the relationship between long and short sequences in terms of their sequence content, enhancer activity, and specificity across melanoma cell states.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE180879.Enhancer activity tables for each library is provided as source data.Scripts used for enhancer - barcode assignment, read processing and activity measurement and analysis are provided in the Scripts directory.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. David Mauduit

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2045-227X
  2. Ibrahim Ihsan Taskiran

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  3. Liesbeth Minnoye

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  4. Maxime de Waegeneer

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  5. Valerie Christiaens

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  6. Gert Hulselmans

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
  7. Jonas Demeulemeester

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2660-2478
  8. Jasper Wouters

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7129-2990
  9. Stein Aerts

    Department of Human Genetics, KU Leuven, Leuven, Belgium
    For correspondence
    stein.aerts@kuleuven.be
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8006-0315

Funding

H2020 European Research Council (724226_cis-CONTROL)

  • Stein Aerts

KU Leuven (C14/18/092)

  • Stein Aerts

Fonds Wetenschappelijk Onderzoek (1S03317N)

  • Liesbeth Minnoye

Fonds Wetenschappelijk Onderzoek (12J6916N)

  • Jonas Demeulemeester

Kom op tegen Kanker

  • Jasper Wouters

H2020 European Research Council (724226_cis-CONTROL)

  • David Mauduit

H2020 European Research Council (724226_cis-CONTROL)

  • Valerie Christiaens

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Jian Xu, University of Texas Southwestern Medical Center, United States

Publication history

  1. Received: June 28, 2021
  2. Preprint posted: July 27, 2021 (view preprint)
  3. Accepted: December 6, 2021
  4. Accepted Manuscript published: December 7, 2021 (version 1)
  5. Version of Record published: December 21, 2021 (version 2)

Copyright

© 2021, Mauduit et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. David Mauduit
  2. Ibrahim Ihsan Taskiran
  3. Liesbeth Minnoye
  4. Maxime de Waegeneer
  5. Valerie Christiaens
  6. Gert Hulselmans
  7. Jonas Demeulemeester
  8. Jasper Wouters
  9. Stein Aerts
(2021)
Analysis of long and short enhancers in melanoma cell states
eLife 10:e71735.
https://doi.org/10.7554/eLife.71735

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