Oncogene-mediated alterations in chromatin conformation David S. Rickmana,1, T. David Soongb,1, Benjamin Mossa, Juan Miguel Mosqueraa, Jan Dlabalb, Stéphane Terrya, Theresa Y. MacDonalda, Joseph Tripodic, Karen Buntingd, Vesna Najfeldc, Francesca Demichelisb,e, Ari M. Melnickd,f, Olivier Elementob,2, and Mark A. Rubina,f,2,3 Departments of aPathology and Laboratory Medicine and dMedicine, bDepartment of Physiology and Biophysics, HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, and fWeill Cornell Cancer Center, Weill Cornell Medical College, New York, NY 10065; cTumor Cytogenetics Laboratory, Department of Pathology, Tisch Cancer Center, Mount Sinai School of Medicine, New York, NY 10029; and eCentre for Integrative Biology, University of Trento, 38122 Trento, Italy Edited* by Eric S. Lander, The Broad Institute of MIT and Harvard, Cambridge, MA, and approved April 24, 2012 (received for review August 3, 2011) Emerging evidence suggests that chromatin adopts a nonrandom Results 3D topology and that the organization of genes into structural ERG Overexpression Is Associated with Chromatin Topology. To test hubs and domains affects their transcriptional status. How chroma- our hypothesis, we used stable isogenic, normal benign prostate tin conformation changes in diseases such as cancer is poorly un- epithelial cell lines (RWPE1) (21) that differ with respect to derstood. Moreover, how oncogenic transcription factors, which ERG overexpression (17) (Fig. S1A). To test whether ERG bind to thousands of sites across the genome, influence gene reg- overexpression is associated with global changes in chromatin ulation by globally altering the topology of chromatin requires structure, we performed unbiased chromatin interaction mapping further investigation. To address these questions, we performed using the Hi-C technique (22) from both RWPE1-ERG and unbiased high-resolution mapping of intra- and interchromosome RWPE1-GFP cells, with biological replicates (Fig. 1A and Fig. interactions upon overexpression of ERG, an oncogenic transcrip- S1A). Successful fill-in and ligation were determined as previously tion factor frequently overexpressed in prostate cancer as a result of reported (22) by testing for a known interaction between two a gene fusion. By integrating data from genome-wide chromosome distant genomic loci located on chromosome 6 (23) (Fig. S1B). conformation capture (Hi-C), ERG binding, and gene expression, we The Hi-C libraries were paired-end sequenced using an Illumina demonstrate that oncogenic transcription factor overexpression is GAIIx platform. Following alignment to the human genome associated with global, reproducible, and functionally coherent (hg18) and filtering to remove unligated and self-ligated DNA, changes in chromatin organization. The results presented here have we identified intrachromosomal (or cis-) and interchromosomal broader implications, as genomic alterations in other cancer types (or trans-) interactions in both RWPE1 cell lines. Correlation frequently give rise to aberrant transcription factor expression, e.g., α matrices obtained from independent biological replicates were EWS-FLI1, c-Myc, n-Myc, and PML-RAR . highly similar in both cell lines (Pearson’s correlation coefficient r = 0.99), indicating that the interaction patterns are highly re- ounting evidence suggests that many genes dynamically producible. Biological replicate interactions were therefore com- Mcolocalize to shared nuclear compartments that favor gene bined for further analyses. In total, we identified 18.4 million activation or silencing (1–3). As demonstrated by chromosome intrachromosomal (or cis-) and 18.3 million interchromosomal (or conformation capture (3C) (4), ligand-bound androgen recep- trans-) interactions in RWPE1-ERG cells (Dataset S1). We also tors (AR) and estrogen receptors mediate looped chromatin identified 16.9 million cis- and 18.6 million trans-interactions in structures resulting in coordinated transcription of target genes RWPE1-GFP cells. To visualize global patterns of cis-interactions, we binned the (5, 6). In embryonic carcinoma cells, the PolyComb complex – subunit EZH2 represses some of its target genes via the for- genome (chromosomes 1 22, X) into 1-Mb intervals and calcu- lated the ratio between observed and expected number of mation of similar looped chromatin structures (7). Trans-inter- interactions connecting each interval pair. We then generated actions that regulate gene expression have also been reported correlation heat maps depicting the extent to which pairs of – (8 10). These data suggest that oncogenic transcriptional regu- genomic intervals interact with the same intervals, on the basis of lators are capable of inducing changes in chromatin structures. the assumption that if two loci are close in nuclear space, their These studies have mainly focused on local chromatin structures, patterns of interaction with other loci should be highly corre- and it is still unclear whether more global changes occur in the lated. Confirming prior observations (22), the heat maps showed process of oncogene-mediated transformation. A broader im- plication of these observations is that global chromatin organi- zation changes could impact functional and phenotypic aspects Author contributions: D.S.R., T.D.S., O.E., and M.A.R. designed research; D.S.R., T.D.S., B.M., J.D., S.T., T.Y.M., J.T., V.N., and O.E. performed research; T.D.S., K.B., F.D., A.M.M., of cancer. and O.E. contributed new reagents/analytic tools; D.S.R., T.D.S., B.M., J.M.M., J.D., S.T., To globally investigate oncogene-mediated chromatin struc- J.T., V.N., O.E., and M.A.R. analyzed data; and D.S.R., T.D.S., J.D., S.T., O.E., and M.A.R. ture changes we focused on ERG, the ETS-family transcription wrote the paper. factor most frequently rearranged and overexpressed in prostate The authors declare no conflict of interest. cancer through the TMPRSS2-ERG and other gene fusions in- *This Direct Submission article had a prearranged editor. volving androgen-responsive promoters (11–13). ERG interacts Freely available online through the PNAS open access option. MEDICAL SCIENCES with several cofactors (14) and other transcription factors in- Data deposition: Hi-C and ChIPseq data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. cluding AR to regulate the expression of thousands of genes that GSE37752). favor dedifferentiation, cell invasion, and neoplastic transforma- 1D.S.R. and T.D.S. contributed equally to this work. – tion of prostate epithelium when overexpressed (15 20). We 2O.E. and M.A.R. contributed equally to this work. therefore hypothesized that changes in global gene expression 3To whom correspondence should be addressed. E-mail: [email protected]. induced by ERG overexpression could be associated with global This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. changes in the 3D structure of chromosomes. 1073/pnas.1112570109/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1112570109 PNAS | June 5, 2012 | vol. 109 | no. 23 | 9083–9088 Downloaded by guest on October 2, 2021 A + ERG abrogated in the presence of ERG (P = 0.01, Fisher’s exact test; Fig. S3D). To test this result, we performed targeted PCR from Remove x-link 3C libraries (3C-PCR) generated from asynchronous cells from Fill (biotin-dCTP) Shear/ Paired-end X-link Hind III Digested Chromatin Ligate Ligated DNA/ pull down Hi-C sequence Hi-C the two cell lines. Consistent with the Hi-C data, the interaction chromatin prep protein library Dataset prep between the promoters of TMPRSS2 and TFF3 was enriched in - ERG control cells (RWPE1-GFP) and depleted in the ERG over- expressing cells (Fig. S3D). One of the most statistically significant cis-interaction changes involved two distant regions on chromosome 6 (regions between B p22.3–12.3 and q22.31–25.32); these regions interact significantly more in cells overexpressing ERG compared with control cells (Fig. 2A and Fig. S3A). We also observed loss of interactions in RWPE1-ERG cells [e.g., chromosome 10 (regions between p15.3– p13 and q21.3–25.1, Fig. S3B) and chromosome 13 (regions be- tween q12.11–13.1 and q13.1–21.1, Fig. S3C)]. Consistent with previous findings (22), we detected more trans-interactions be- tween small, gene-rich chromosomes (e.g., chromosomes 16–22) than between larger chromosomes in both RWPE1-ERG and − − RWPE1-GFP cells (P =1.4× 10 9 and P =4.1× 10 6,re- spectively, Mann–Whitney tests; Fig. S4A). Moreover, specific regions of chromosomes tended to interact preferentially on the basis of high-resolution heat maps of normalized interactions be- tween all cytogenetic bands (Fig. S4B). RWPE-1 cells have been reported to be primarily diploid and to harbor specific trans- locations involving chromosomes 9, 12, 18, and 21 in at least 90% of the cells (21). To determine whether additional, unreported translocations accounted for the enriched Hi-C interactions, we performed spectral karyotyping of both cell lines (24). The kar- yotypes observed in the two cell lines were identical, barring a der (13)t(13;15)(q12;q12) unique to ERG overexpressing cells (Fig. S5A), and also detectable using chromosome painting (Fig. S5B). Accordingly, our Hi-C data show a specific increase in interaction between chromosome 13 and chromosome 15 in RWPE1-ERG Fig. 1. Specific cis-interactions that depend on ERG expression. (A) Sche- cells (Figs. S4B and S5C). The spectral karyotyping results thus matic representation of the experimental flow of the Hi-C experiments. Red indicate that changes in interchromosomal interactions detected symbols refer to ERG protein and white symbols refer to other DNA-inter- by Hi-C sometimes represent translocations. However, further acting proteins. (B) Circos plot depicting chromosomes 1–22 and X anno- inspection of the Hi-C and spectral karyotype data shows that tated for ERG binding on the basis of ChIP-seq data (normalized reads shown several ERG- or GFP-specific trans-interactions revealed by Hi-C in orange) and 1,266 differentially expressed genes annotated on the basis are unlikely to be translocations.