Transcriptomics

Dataset Information

296

Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates (CEL small RNA)


ABSTRACT: 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. small RNAs were extracted from total RNA of lysed worms. Standard small RNA sequencing was performed to sequence 5' monophosphate bearing small RNAs. Alternatively, 5'polyphosphatase from Epicenter was used to catch also tri-phosphate bearing secondary endo-siRNAs.

ORGANISM(S): Caenorhabditis elegans  

SUBMITTER: Nikolaus Rajewsky   Yasuhiro Murakawa  Agnieszka Rybak-Wolf  Marvin Jens  Markus Landthaler 

PROVIDER: E-GEOD-55332 | ArrayExpress | 2014-11-20

SECONDARY ACCESSION(S): GSE55332SRP038926PRJNA239337

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

A variety of dicer substrates in human and C. elegans.

Rybak-Wolf Agnieszka A   Jens Marvin M   Murakawa Yasuhiro Y   Herzog Margareta M   Landthaler Markus M   Rajewsky Nikolaus N  

Cell 20141101 5


The endoribonuclease Dicer is known for its central role in the biogenesis of eukaryotic small RNAs/microRNAs. Despite its importance, Dicer target transcripts have not been directly mapped. Here, we apply biochemical methods to human cells and C. elegans and identify thousands of Dicer-binding sites. We find known and hundreds of additional miRNAs with high sensitivity and specificity. We also report structural RNAs, promoter RNAs, and mitochondrial transcripts as Dicer targets. Interestingly,  ...[more]

Similar Datasets

2014-11-20 | E-GEOD-55325 | ArrayExpress
2014-11-20 | E-GEOD-55329 | ArrayExpress
2014-11-20 | E-GEOD-55331 | ArrayExpress
2014-11-20 | E-GEOD-55324 | ArrayExpress
2014-11-20 | E-GEOD-55326 | ArrayExpress
| GSE55325 | GEO
2014-11-20 | E-GEOD-63437 | ArrayExpress
2014-11-20 | E-GEOD-63458 | ArrayExpress
2014-11-20 | E-GEOD-63435 | ArrayExpress
2014-11-20 | E-GEOD-63475 | ArrayExpress