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Series GSE55325 Query DataSets for GSE55325
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
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.
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.
Contributor(s) Rybak-Wolf A, Jens M, Murakawa Y, Landthaler M, Rajewsky N
Citation(s) 25416952
Submission date Feb 25, 2014
Last update date May 15, 2019
Contact name Marvin Jens
Phone +493094062989
Organization name Max Delbrueck Center for Molecular Medicine
Department Systems Biology of Gene Regulatory Elements
Lab Rajewsky lab
Street address Robert Rössle Str. 10 (H. 87)
City Berlin
ZIP/Postal code 13092
Country Germany
Platforms (1)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
Samples (3)
GSM1334290 PAR-CLIP with T1/V1, replicate 1
GSM1334291 PAR-CLIP with T1/V1, replicate 2
GSM1334292 PAR-CLIP with T1 (replicate 3)
This SubSeries is part of SuperSeries:
GSE55333 Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates
BioProject PRJNA239325
SRA SRP038920

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Supplementary file Size Download File type/resource
GSE55325_RAW.tar 170.0 Kb (http)(custom) TAR (of GFF)
GSE55325_dcr-1_consensus.gff.gz 352.6 Kb (ftp)(http) GFF
GSE55325_dcr-1_conservative.gff.gz 196.5 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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