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| Status |
Public on May 23, 2012 |
| Title |
Oncogene-Mediated Alterations in Chromatin Conformation |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Emerging evidence suggests that chromatin adopts a non-random three-dimensional (3D) topology and that the organization of genes into structural hubs and domains affects their transcriptional status. How chromatin conformation changes in diseases such as cancer is poorly understood. Moreover, how oncogenic transcription factors, which bind to thousands of sites across the genome, influence gene regulation by globally altering the topology of chromatin requires further investigation. To address these questions, we performed unbiased high-resolution mapping of intra- and inter-chromosome interactions upon over-expression of ERG, an oncogenic transcription factor frequently over-expressed in prostate cancer as a result of a gene fusion. By integrating data from genome-wide chromosome conformation capture (Hi-C), ERG binding and gene expression, we demonstrate that oncogenic transcription factor over-expression is associated with global, reproducible and functionally coherent changes in chromatin organization. The results presented here have broader implications, as genomic alterations in other cancer types frequently give rise to aberrant transcription factor expression e.g., EWS-FLI1, c-Myc, n-Myc, PML-RARĪ±.
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| Overall design |
We used stable isogenic, normal benign prostate epithelial cell lines (RWPE1) that differ with respect to ERG3 over-expression. To test whether ERG over-expression is associated with global changes in chromatin structure, we performed unbiased chromatin interaction mapping using the Hi-C technique from both RWPE1-ERG and RWPE1-GFP cells, with biological replicates. Successful fill-in and ligation were determined as previously reported by testing for a known interaction between two distant genomic loci located on chromosome 6. The Hi-C libraries were paired-end sequenced using an Illumina GAIIx platform. Following alignment to the human genome (hg18) and filtering to remove un-ligated and self-ligated DNA, we identified intra-chromosomal (or cis-) and inter-chromosomal (or trans-) interactions in both RWPE1 cell lines. To characterize ERG binding and ERG-mediated gene expression changes in these cells, we performed chromatin-immunoprecipitation combined with high-throughput sequencing (ChIP-seq) and RNA sequencing (RNA-seq). ERG was bound to 6,398 sites in RPWE1-ERG cells. Based on paired-end RNA-seq data from both cell lines, 1,266 genes were differentially expressed between RWPE1-ERG and RWPE1-GFP cell lines.
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| Contributor(s) |
Rickman DS, Soong D, Moss B, Mosquera JM, Dlabal J, Terry S, MacDonald TY, Tripodi J, Bunting K, Najfeld V, Demichelis F, Melnick AM, Elemento O, Rubin MA |
| Citation(s) |
22615383 |
| Submission date |
May 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
David Soong |
| Organization name |
Weill Cornell Medical College
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| Department |
Institute for Computational Biomedicine
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| Street address |
1305 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA163079 |
| SRA |
SRP012651 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37752_ERG_inter.sif.gz |
312.1 Mb |
(ftp)(http) |
SIF |
| GSE37752_ERG_intra.bed.gz |
452.3 Mb |
(ftp)(http) |
BED |
| GSE37752_GFP_inter.sif.gz |
317.5 Mb |
(ftp)(http) |
SIF |
| GSE37752_GFP_intra.bed.gz |
416.3 Mb |
(ftp)(http) |
BED |
| GSE37752_RAW.tar |
420.0 Kb |
(http)(custom) |
TAR (of TXT) |
| GSE37752_TF_targets1_2_t10_ChIPseeqer.txt.gz |
186.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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