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| Status |
Public on Jan 01, 2008 |
| Title |
Epigenetically Silenced Genes Found Using Methylated DNA Immunoprecipitation in Colon Cancer Cells Deficient in DNMTs |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
|
| Summary |
CpG island promoter hypermethylation of tumor suppressor genes is a common hallmark of human cancer, and new large-scale epigenomic technologies might be useful in our attempts to define the complete DNA hypermethylome of tumor cells. Here we report a functional search for hypermethylated CpG islands using the colorectal cancer cell line HCT-116, in which two major DNA methyltransferases, DNMT1 and DNMT3b, have been genetically disrupted (DKOcells). Using methylated DNA immunoprecipitation (MeDIP) methodology in conjunction with promoter microarray analyses we found that DKO cells experience a significant loss of hypermethylated CpG islands. Further characterization of these candidate sequences demonstrates CpG island promoter hypermethylation and silencing of genes with potentially important roles in tumorigenesis, such as the Ras guanine-nucleotide release factor RASGRF2, the apoptosis-associated basic helixloop transcription factor BHLHB9, and the homeobox gene HOXD1. Hypermethylation of these genes occurs already in premalignant lesions and accumulates during tumorigenesis. Thus, our results demonstrate the usefulness of DNMT genetic disruption strategies combined with MeDIP in searching for unknown hypermethylated candidate genes in human cancer that might aid our understanding of the biology of the disease and be of potential translational use.
Keywords: Human Proximal Promoter Array; DNA Methylation
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| Overall design |
Comparative experiment: methylated DNA immunoprecipitated/INPUT(Total Genomic DNA) from the colon cancer cell line HCT116 wild type vs methylated DNA imonoprecipitated/INPUT from the colon cancer cell line HCT116 DNMT1/3b doubleknockout (DKO)
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| Contributor(s) |
Esteller M, Jacinto FV |
| Citation(s) |
18089774 |
| Submission date |
Oct 09, 2007 |
| Last update date |
Mar 17, 2012 |
| Contact name |
Filipe Vicente Jacinto |
| E-mail(s) |
fvjacinto@cnio.es
|
| Phone |
+ (34) 912 246 964
|
| Fax |
+ (34) 912 246 980
|
| Organization name |
CNIO
|
| Department |
Molecular Pathology
|
| Lab |
Cancer Epigenetics
|
| Street address |
C/ Melchor Fernández Almagro, 3,
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
E-28029 |
| Country |
Spain |
| |
|
| Platforms (2) |
| GPL4089 |
Agilent-013902 Human Proximal Promoter ChIP-on-Chip Set, Microarray 1 of 2 G4481A |
| GPL4090 |
Agilent-013903 Human Proximal Promoter ChIP-on-Chip Set, Microarray 2 of 2 G4481A |
|
| Samples (4)
|
| GSM235386 |
methylated DNA Immunoprecipitation/INPUT HCT116 wild type - array 1 of 2 |
| GSM235387 |
methylated DNA Immunoprecipitation/INPUT HCT116 DNMT1/3b doubleknockout (DKO) - array 1of 2 |
| GSM235388 |
methylated DNA Immunoprecipitation/INPUT HCT116 wild type- array 2 of 2 |
| GSM235389 |
methylated DNA Immunoprecipitation/INPUT HCT116 DNMT1/3b doubleknockout (DKO) - array 2 of 2 |
|
| Relations |
| BioProject |
PRJNA102899 |
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