Abstract LB-249: Oncogene-mediated alterations in chromatin conformation
Authors: Rickman David S. , Soong Ta-tsen David , Moss Benjamin , Kitabayashi Naoki , Bunting Karen , Naseeruddin Saif , Garraway Levi A. , Berger Michael F. , Melnick Ari , Elemento Olivier , Rubin Mark A. 
Published: June 2012

Emerging evidence suggests that the three-dimensional structure of chromosomes is not random but rather organized into compartments of open and closed chromatin and that this architectural organization plays a major role in gene regulation and genomic aberrations. There is evidence that transcription factors mediate chromatin topology and have been implicated in DNA breaks leading to genomic rearrangement. However, no study, to date, has described a comprehensive, genome-wide characterization of chromatin topological changes, gene regulation, and genomic alterations that can be attributed to oncogenic transcription factors. ETS rearranged prostate cancers, similar to other translocation tumors, represent a common and distinct molecular subclass of PCa based on studies demonstrating characteristic morphologic features, natural history and specific genomic and expression profiles. We hypothesize that ERG mediates specific alterations in chromatin structure that translates into changes in gene expression and genomic alterations in prostate cancer. We used next-generation DNA sequencing and chromosome conformation capture technology (Hi-C) to systematically map long-range chromatin interactions in the prostate cancer genomes of isogenic cell lines that differ in respect to ERG over-expression. Two biological replicate HiC samples were sequenced using five lanes of an Illumina GAIIx flow cell per cell line. After filtering, we obtained a total of roughly 20 million paired end sequence reads that corresponded to intra- and interchromosome interactions per cell line. We validated specific long-range interactions using targeted PCR from 3C libraries and using fluorescent in situ hybridization (FISH). In addition, we performed chromatin-immunoprecipitation with DNA sequencing (ChIPseq) and next generation RNA sequencing (RNA-seq) on the same cell lines to evaluate areas of ERG binding, determine the landscape of histone marks and quantify differential mRNA expression. We identified chromosomal interactions that appear to be dependent on ERG expression and these interactions are associated with ERG binding and changes in gene expression. Finally, we performed an integrative analysis of available whole genome DNA sequencing data (30 x coverage) from 7 prostate cancer samples (Berger et al., Nature 2011) and found associations between mapped genomic rearrangement, ERG binding and cell line specific long range chromosome interactions. Our study indicates, for the first time, that oncogenic transcription factors exert a broad effect on chromatin topology and associated gene regulation, and suggest that chromatin conformation predisposes the genome for later rearrangement events.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-249. doi:10.1158/1538-7445.AM2011-LB-249