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E-GEOD-55324 - Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (HEK PAR-CLIP)

Status
Released on 20 November 2014, last updated on 23 December 2014
Organism
Homo sapiens
Samples (3)
Protocols (2)
Description
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. PAR-CLIP basically as described previously (Hafner et al. 2010).
Experiment types
other, RNA-seq of non coding RNA 
Contacts
Marvin Jens <marvin.jens@mdc-berlin.de>, Agnieszka Rybak-Wolf, Markus Landthaler, Nikolaus Rajewsky, Yasuhiro Murakawa
Citation
A Variety of Dicer Substrates in Human and C.�elegans. Rybak-Wolf A, Jens M, Murakawa Y, Herzog M, Landthaler M, Rajewsky N. , PMID:25416952
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-55324.idf.txt
Sample and data relationshipE-GEOD-55324.sdrf.txt
Processed data (1)E-GEOD-55324.processed.1.zip
Additional data (1)E-GEOD-55324.additional.1.zip
Links