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| Status |
Public on Sep 27, 2011 |
| Title |
Regions of Focal DNA Hypermethylation and Long-Range Hypomethylation in Colorectal Cancer Coincide with Nuclear Lamina-Associated Domains |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Extensive changes in DNA methylation are common in cancer and may contribute to oncogenesis through transcriptional silencing of tumor suppressor genes. Genome-scale studies have yielded important insights into these changes, but have focused on CpG islands or gene promoters. We used whole-genome bisulfite sequencing (Bisulfite-Seq) to comprehensively profile a primary human colorectal tumor and adjacent-normal colon tissue at single-basepair resolution. Regions of focal hypermethylation in the tumor were located primarily at CpG islands and were concentrated within regions of long-range (>100 kb) hypomethylation. These hypomethylated domains covered nearly half the genome and coincided with late replication and attachment to the nuclear lamina in human cell lines. The confluence of hypermethylation and hypomethylation within these domains was confirmed in 25 diverse colorectal tumors with matched adjacent tissue. We propose that widespread DNA methylation changes in cancer are linked to silencing programs orchestrated by the 3D organization of chromatin within the nucleus.
dbGAP study: phs000385
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| Overall design |
Primary tissue samples sequenced using 76-bp bisulfite sequencing (WGBS or Methyl-seq) using the Illumina GAII platform. Two independent libraries were constructed for each sample, and these libraries were combined into a single data file for each sample.
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| Contributor(s) |
Berman B, Weisenberger DJ, Laird PW |
| Citation(s) |
22120008 |
| Submission date |
Sep 26, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin Berman |
| E-mail(s) |
bberman@usc.edu
|
| Organization name |
University of Southern California
|
| Department |
USC Epigenome Center
|
| Street address |
1450 Biggy St. #G511
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (2) |
| GSM801956 |
Normal colonic mucosa adjacent to CIMP-H tumor |
| GSM801957 |
Stage 3, CIMP-H colon tumor with G12D KRAS mutation |
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| Relations |
| SRA |
SRP007649 |
| BioProject |
PRJNA147931 |
