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| Status |
Public on Jan 25, 2007 |
| Title |
Identification of genes directly regulated by the oncogene ZNF217 using ChIP-chip assays |
| Project |
Pilot ENCODE
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| Organism(s) |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
It has been proposed that ZNF217, which is amplified at 20q13 in various tumors, plays a key role during neoplastic transformation. ZNF217 has been purified in complexes that contain repressor proteins such as CtBP2, suggesting that it acts as a transcriptional repressor. However, the function of ZNF217 has not been well characterized due to a lack of known target genes. Using a global ChIP-chip approach, we have identified thousands of ZNF217 binding sites in three tumor cell lines (MCF7, SW480, and Ntera2). Further analysis of ZNF217 in Ntera2 cells has shown that many promoters are bound by ZNF217 and CtBP2, and that a subset of these promoters are activated upon removal of ZNF217. Thus, our in vivo studies corroborate the in vitro biochemical analyses of ZNF217-containing complexes and support the hypothesis that ZNF217 functions as transcriptional repressor. Gene ontology analysis shows that ZNF217 targets in Ntera2 cells are involved in organ development, suggesting that one function of ZNF217 may be to repress differentiation. Accordingly, we show that differentiation of Ntera2 cells with retinoic acid leads to downregulation of ZNF217. Our identification of thousands of ZNF217 target genes will enable further studies of the consequences of aberrant expression of ZNF217 during neoplastic transformation.
Keywords: ChIP-chip
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| Overall design |
ChIP-chip assays using antibody of ZNF217 on ENCODE arrays
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| Web Link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
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| Contributor(s) |
Krig SR, Jin VX, Bieda MC, O'Geen H, Green R, Farnham PJ |
| Citation(s) |
17259635
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| Submission date |
Jan 02, 2007 |
| Contact name |
Victor X Jin |
| E-mail(s) |
vxjin@ucdavis.edu
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| Phone |
530-7549729
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| Organization name |
UC Davis
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| Department |
Genome Center
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| Lab |
Peggy J. Farnham
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| Street address |
One Shields Ave. GBSF 4502
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platforms (1) |
| GPL3980 |
UC Davis Human ENCODE array |
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| Samples (11)
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| GSM153604 |
Human MCF-7 cells, ZNF217 Replicate A |
| GSM153605 |
Human MCF-7 cells, ZNF217 Replicate B |
| GSM153606 |
Human MCF-7 cells, ZNF217 Replicate C |
| GSM153607 |
Human Ntera2 cells, ZNF217 Replicate C |
| GSM153608 |
Human Ntera2 cells, ZNF217 Replicate B |
| GSM153609 |
Human Ntera2 cells, ZNF217 Replicate A |
| GSM153610 |
Human SW480 cells, ZNF217 Replicate A |
| GSM153611 |
Human SW480 cells, ZNF217 Replicate B |
| GSM153612 |
Human SW480 cells, ZNF217 Replicate C |
| GSM153613 |
Human Ntera2 cells, siZNF217 Knockout |
| GSM153614 |
Human Ntera2 cells, siZNF217 Control |
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| This SubSeries is part of SuperSeries: |
| GSE6634 |
Genes Directly Regulated by the Oncogene ZNF217 Using ChIP-chip Assays on ENCODE and Promoter Arrays and Expression Data |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE6624_RAW.tar |
141.1 Mb |
(ftp)(http) |
TAR (of TXT) |
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