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, 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 of the miRNA pathway.
Sample name | Organism | Experiment title | Sample type | Library instrument | Attributes | |||||||||||||||||||||||||||||||||||||||||||||||||
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cell line | development stage | genotype | knockdown | source name | strain | transfection | ||||||||||||||||||||||||||||||||||||||||||||||||
PAR-CLIP with T1 (replicate 3) | Caenorhabditis elegans | GSM1334292: PAR-CLIP with T1 (replicate 3); Caenorhabditis elegans; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | young adult whole worm | FLAG:DCR-1 | ||||||||||||||||||||||||||||||||||||||||||||||||
PAR-CLIP with T1/V1, replicate 2 | Caenorhabditis elegans | GSM1334291: PAR-CLIP with T1/V1, replicate 2; Caenorhabditis elegans; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | young adult whole worm | FLAG:DCR-1 | ||||||||||||||||||||||||||||||||||||||||||||||||
PAR-CLIP with T1/V1, replicate 1 | Caenorhabditis elegans | GSM1334290: PAR-CLIP with T1/V1, replicate 1; Caenorhabditis elegans; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | young adult whole worm | FLAG:DCR-1 | ||||||||||||||||||||||||||||||||||||||||||||||||
FLAG:AGO3 loaded small RNA | Homo sapiens | GSM1334331: FLAG:AGO3 loaded small RNA; Homo sapiens; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | HEK293 | cell culture | HEK293 T-Rex | |||||||||||||||||||||||||||||||||||||||||||||||
FLAG:AGO2 loaded small RNA | Homo sapiens | GSM1334330: FLAG:AGO2 loaded small RNA; Homo sapiens; RNA-Seq | RNA-Seq | Illumina HiSeq 2000 | HEK293 | cell culture | HEK293 T-Rex |