title: Functional chromatin features are associated with structural mutations in cancer.
abstract: BACKGROUND
  Structural mutations (SMs) play a major role in cancer development. In some cancers, such as breast and ovarian, DNA double-strand breaks (DSBs) occur more frequently in transcribed regions, while in other cancer types such as prostate, there is a consistent depletion of breakpoints in transcribed regions. Despite such regularity, little is understood about the mechanisms driving these effects. A few works have suggested that protein binding may be relevant, e.g. in studies of androgen receptor binding and active chromatin in specific cell types. We hypothesized that this behavior might be general, i.e. that correlation between protein-DNA binding (and open chromatin) and breakpoint locations is common across divergent cancers.
  
  
  RESULTS
  We investigated this hypothesis by comprehensively analyzing the relationship among 457 ENCODE protein binding ChIP-seq experiments, 125 DnaseI and 24 FAIRE experiments, and 14,600 SMs from 8 diverse cancer datasets covering 147 samples. In most cancers, including breast and ovarian, we found enrichment of protein binding and open chromatin in the vicinity of SM breakpoints at distances up to 200 kb. Furthermore, for all cancer types we observed an enhanced enrichment in regions distant from genes when compared to regions proximal to genes, suggesting that the SM-induction mechanism is independent from the bias of DSBs to occur near transcribed regions. We also observed a stronger effect for sites with more than one protein bound.
  
  
  CONCLUSIONS
  Protein binding and open chromatin state are associated with nearby SM breakpoints in many cancer datasets. These observations suggest a consistent mechanism underlying SM locations across different cancers.
authors.forename: Krzysztof R
authors.initials: KR
authors.lastname: Grzeda
authors.forename: Beryl
authors.initials: B
authors.lastname: Royer-Bertrand
authors.forename: Koichiro
authors.initials: K
authors.lastname: Inaki
authors.forename: Hyunsoo
authors.initials: H
authors.lastname: Kim
authors.forename: Axel M
authors.initials: AM
authors.lastname: Hillmer
authors.forename: Edison T
authors.initials: ET
authors.lastname: Liu
authors.affiliation: The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06030, USA. jeff.chuang@jax.org.
authors.forename: Jeffrey H
authors.initials: JH
authors.lastname: Chuang
mesh_terms: D020029:Base Pairing; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D053903:DNA Breaks, Double-Stranded; D006801:Humans; D008297:Male; D009154:Mutation / Q000235:genetics*; D009363:Neoplasm Proteins / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics*; D016017:Odds Ratio; D011485:Protein Binding
chemical_list: D002843:Chromatin; D009363:Neoplasm Proteins