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| Status |
Public on Nov 20, 2014 |
| Title |
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL PAR-CLIP) |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Other
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Dicer is a deeply conserved endoribonuclease with key functions in small RNA biogenesis. Here we employed PAR-CLIP/iPAR-CLIP to identify direct Dicer binding sites in the transcriptomes of human cells and human. We found hundreds of novel miRNAs and non-canonical Dicer substrates with high sensitivity. Small RNA production depended on structure of the binding site and is globally biased towards the 5' arm of hairpins. Unexpectedly, in both species Dicer bound numerous hairpins inside mRNAs without observable small RNA production. Our data revealed ~100 mRNAs of protein coding genes to be targeted in both human and worm. These mRNAs significantly overlapped with the RNAi pathway. We also, unexpectedly, found that mitochondrial transcripts are Dicer targets in both species. We demonstrate functional consequences of Dicer binding by perturbation analysis. Taken together,we provide the first genome-wide catalog of direct Dicer targets. Our results suggest widespread function outside of miRNA biogenesis.
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| Overall design |
In vivo PAR-CLIP basically as described previously (Jungkamp et al. 2011). FLAG tagged DCR-1 expressing (rescue strain) and 4SU labeled animals were UV irradiated at young adult stage. Worm lysate (NP40) was treated with RNase T1 and RNase V1. After that, PAR-CLIP proceeded as described in Hafner et al. 2010.
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| Contributor(s) |
Rybak-Wolf A, Jens M, Murakawa Y, Landthaler M, Rajewsky N |
| Citation(s) |
25416952 |
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| Submission date |
Feb 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Marvin Jens |
| E-mail(s) |
marvin.jens@mdc-berlin.de
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| Phone |
+493094062989
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| Organization name |
Max Delbrueck Center for Molecular Medicine
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| Department |
Systems Biology of Gene Regulatory Elements
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| Lab |
Rajewsky lab
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| Street address |
Robert Rössle Str. 10 (H. 87)
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| City |
Berlin |
| ZIP/Postal code |
13092 |
| Country |
Germany |
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| Platforms (1) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE55333 |
Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates |
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| Relations |
| BioProject |
PRJNA239325 |
| SRA |
SRP038920 |
