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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 27, 2013 |
| Title |
Genome-wide profiling of Argonaute-chromosome interactions [ChIP-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Argonuate proteins are the central components of the RNA-induced silencing complex (RISC) which execute small RNA-mediated gene regulation mainly in the cytoplasm and their nuclear functions in mammalian cells remain largely unknown. Here we show that in human cancer cells Ago1 is pervasively associated with chromosomal loci throughout the genome with the association centered mostly on actively transcribed promoters. Ago1 but not Ago2 physically interacts with RNA polymerase II (RNAP II) in the nucleus. Moreover, genes bound by Ago1 are significantly enriched for several cancer related pathways. Detailed analysis of these genes including PIK3CA, PRKCH, CDC6 and RRM1 verified Ago1-mediated transcriptional gene regulation through Ago1-promoter interactions. We also found a strong correlation between Ago1-bound genes and genes downregulated by Ago1 depletion which, phenotypically, leads to inhibition of proliferation in different cancer cells. Therefore, our findings reveal the first landscape of human Ago1-chromosomal interactions which may drive oncogenic programs in cancer cells
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| Overall design |
Examination of Ago-DNA interactions in human cancer cells
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| Contributor(s) |
Huang V, Zheng J, Li L, Li H |
| Citation(s) |
24086155 |
| Submission date |
Aug 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Vera Huang |
| E-mail(s) |
vhuang2013@gmail.com
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| Organization name |
UCSF
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| Department |
Urology
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| Lab |
Long-Cheng Li Lab
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| Street address |
1450 Third Street, Helen Diller Cancer Research Building, Room 302
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA174235 |
| SRA |
SRP015340 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40536_RAW.tar |
582.9 Mb |
(http)(custom) |
TAR (of BED, TXT, WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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