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Epigenetic Analysis in Ewing Sarcoma

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Book cover Ewing Sarcoma

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2226))

Abstract

Ewing sarcoma is a highly malignant tumor characterized by a chromosomal translocation that modifies the activity of an ETS family transcription factor. The most prevalent translocation product, EWSR1-FLI1, exploits a permissive and unique chromatin environment of stem cells, and transforms them into an oncogenic state through alterations to gene expression and gene regulatory programs. Though the transformation ability of, and subsequent reliance on EWSR1-FLI1 had been previously described, the advent of genome-wide sequencing technologies allowed for the specific identification of genomic loci and genes targeted by EWSR1-FLI1. Furthermore, the characterization of the chromatin environment in these, and other, cell types could not have been accomplished without the computational and statistical methods that enable large-scale data analysis. Here, we outline in detail the tools and steps needed to analyze genome-wide transcription factor binding and histone modification data (chromatin immunoprecipitation, ChIP-seq), as well as chromatin accessibility data (assay for transposase-accessible chromatin, ATAC-seq) from Ewing sarcoma cells. Our protocol includes a compilation of data quality control metrics, trimming of adapter sequences, reference genome alignment, identification of enriched sites (“peaks”) and motifs, as well as annotation and visualization, using real-world data. These steps should provide a platform on which molecular biologists can build their own analytical pipelines to aid in data processing, analysis, and interpretation.

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Acknowledgments

We would like to thank Y Yang and L Whitehouse for constructive comments. J.M.S. was supported by The Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD079124) and NINDS (P30NS045892). N.C.G. holds a Postdoctoral Enrichment Program Award from the Burroughs Wellcome Fund and is supported by a NIH Postdoctoral Ruth L. Kirschstein National Research Service Award F32CA221353.

Author information

Authors and Affiliations

  1. Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

    Jeremy M. Simon

  2. Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

    Jeremy M. Simon

  3. UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA

    Jeremy M. Simon

  4. Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA

    Nicholas C. Gomez

Authors
  1. Jeremy M. Simon
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  2. Nicholas C. Gomez
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Corresponding author

Correspondence to Nicholas C. Gomez .

Editor information

Editors and Affiliations

  1. Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ) Hopp-Children’s Cancer Center (KiTZ), Heidelberg, Germany

    Florencia Cidre-Aranaz

  2. Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), Hopp-Children’s Cancer Center (KiTZ), Heidelberg, Germany

    Thomas G. P. Grünewald

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Simon, J.M., Gomez, N.C. (2021). Epigenetic Analysis in Ewing Sarcoma. In: Cidre-Aranaz, F., G. P. Grünewald, T. (eds) Ewing Sarcoma . Methods in Molecular Biology, vol 2226. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1020-6_22

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  • DOI: https://doi.org/10.1007/978-1-0716-1020-6_22

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1019-0

  • Online ISBN: 978-1-0716-1020-6

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