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| Status |
Public on Jul 31, 2009 |
| Title |
The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
Genome binding/occupancy profiling by genome tiling array
Expression profiling by array
|
| Summary |
Instructive mechanisms are present for induction of DNA methylation, as shown by methylation of specific CpG islands (CGIs) by specific inducers and in specific cancers. However, instructive factors involved are poorly understood, except for involvement of low transcription and trimethylation of histone H3 lysine 27 (H3K27me3). Here, we used methylated DNA immunoprecipitation (MeDIP) combined with a CGI oligonucleotide microarray analysis, and identified 5510 and 521 genes with promoter CGIs resistant and susceptible, respectively, to DNA methylation in prostate cancer cell lines. Expression analysis revealed that the susceptible genes had low transcription in a normal prostatic epithelial cell line. Chromatin immunoprecipitation with microarray hybridization (CHiP-chip) analysis of RNA polymerase II (Pol II) and histone modifications showed that, even among the genes with low transcription, the presence of Pol II was associated with marked resistance to DNA methylation (OR = 0.22; 95% CI = 0.12-0.38), and H3K27me3 was associated with increased susceptibility (OR = 11.20; 95% CI = 7.14-17.55). The same was true in normal human mammary epithelial cells for 5430 and 733 genes resistant and susceptible, respectively, to DNA methylation in breast cancer cell lines. These results showed that the presence of Pol II, active or stalled, and H3K27me3 can predict the epigenetic fate of promoter CGIs independently of transcription levels.
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| Overall design |
To analyze DNA methylation status in normal and cancer cells, MeDIP-CGI oligonucleotide microarray analysis was performed. To analyze expression and histone modification status in normal cells, GeneChip analysis and ChIP-oligonucleotide microarray analysis were performed.
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| Citation(s) |
19652013 |
| |
| Submission date |
Mar 09, 2009 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Hideyuki Takeshima |
| E-mail(s) |
takeshima.hideyuki@hoshi.ac.jp
|
| Organization name |
Hoshi University
|
| Department |
Institute for Advanced Life Sciences
|
| Lab |
Department of Epigenomics
|
| Street address |
2-4-41 Ebara
|
| City |
Shinagawa-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
142-8501 |
| Country |
Japan |
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| Platforms (2) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL4126 |
Agilent-014791 Human CpG Island ChIP-on-Chip Microarray 244K (G4492A) (Feature Number version) |
|
| Samples (21)
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| GSM375642 |
DNA methylation of CpG island in PC3 |
| GSM375643 |
DNA methylation of CpG island in LNCaP |
| GSM375644 |
DNA methylation of CpG island in 22Rv1 |
|
| Relations |
| BioProject |
PRJNA114921 |
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