Transcriptomics

Dataset Information

297

A variety of Dicer substrates in human and C. elegans (HEK RNA-seq)


ABSTRACT: 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 novel miRNAs with high sensitivity and specificity. We also report structural RNAs, promoter RNAs, and mitochondrial transcripts as Dicer targets. Interestingly, most Dicer binding sites reside on mRNAs/lncRNAs and are not significantly processed into small RNAs. These passive sites typically harbor small, Dicer-bound hairpins within intact transcripts and generally stabilize target expression. We show that passive sites can sequester Dicer and reduce microRNA expression. mRNAs with passive sites were in human and worm significantly associated with processing-body/granule function. Together, we provide the first transcriptome-wide map of Dicer targets and suggest conserved binding modes and functions outside the miRNA pathway. Regulatory impact of Dicer binding was assessed by knock down experiments in human HEK293 cells. Drosha knockdown and mock transfections were used as controls. Knockdown was performed with two independent siRNAs each. In total 5 samples.

ORGANISM(S): Homo sapiens  

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

PROVIDER: E-GEOD-63475 | ArrayExpress | 2014-11-20

SECONDARY ACCESSION(S): SRP050055GSE63475PRJNA268010

REPOSITORIES: GEO, ArrayExpress, ENA

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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]

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