1. Computational and Systems Biology

A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference

  1. Dina Cramer
  2. Luis Serrano  Is a corresponding author
  3. Martin H Schaefer  Is a corresponding author
  1. The Barcelona Institute of Science and Technology, Spain
https://doi.org/10.7554/eLife.16519
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  1. Dina Cramer
  2. Luis Serrano
  3. Martin H Schaefer
(2016)
A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference
eLife 5:e16519.
https://doi.org/10.7554/eLife.16519
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Abstract

Copy number alterations (CNAs) in cancer patients show a large variability in their number, length and position. CNA number and length are linked to patient survival suggesting clinical relevance. However, the sources of this variability are not known. We have identified genes that tend to be mutated in samples having few or many CNAs, which we term CONIM genes (COpy Number Instability Modulators). CONIM proteins cluster into a densely connected subnetwork of physical interactions and many of them are epigenetic modifiers. Therefore, we investigate how the epigenome of the tissue-of-origin influences the position of CNA breakpoints and the properties of the resulting CNAs. We find that the presence of heterochromatin in the tissue-of-origin contributes to the recurrence and length of CNAs in the respective cancer type.

Data availability

The following previously published data sets were used
    1. Kundaje
    2. A. et al.
    (2015) Histone ChIP-seq peaks
    Publicly available at NIH Roadmap Epigenomics Mapping Consortium.
    http://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/narrowPeak/

Article and author information

Author details

  1. Dina Cramer

    EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
    Competing interests
    The authors declare that no competing interests exist.

  2. Luis Serrano

    EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
    For correspondence
    luis.serrano@crg.eu
    Competing interests
    The authors declare that no competing interests exist.

  3. Martin H Schaefer

    EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
    For correspondence
    martin.schaefer@crg.eu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7503-6364

Funding

Deutsche Forschungsgemeinschaft (SCHA 1933/1-1)

  • Martin H Schaefer

European Commission (HEALTH-F4-2011-278568)

  • Luis Serrano

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

Reviewing Editor

  1. Jason Ernst, University of California, Los Angeles, United States

Version history

  1. Received: March 30, 2016
  2. Accepted: November 2, 2016
  3. Accepted Manuscript published: November 10, 2016 (version 1)
  4. Version of Record published: November 24, 2016 (version 2)

Copyright

© 2016, Cramer 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. Dina Cramer
  2. Luis Serrano
  3. Martin H Schaefer
(2016)
A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference
eLife 5:e16519.
https://doi.org/10.7554/eLife.16519

Share this article

https://doi.org/10.7554/eLife.16519

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