例如:"lncRNA", "apoptosis", "WRKY"

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

Cell. 2014 Nov 20;159(5):1153-1167
Agnieszka Rybak-Wolf 1 , Marvin Jens 1 , Yasuhiro Murakawa 2 , Margareta Herzog 1 , Markus Landthaler 3 , Nikolaus Rajewsky 4
Agnieszka Rybak-Wolf 1 , Marvin Jens 1 , Yasuhiro Murakawa 2 , Margareta Herzog 1 , Markus Landthaler 3 , Nikolaus Rajewsky 4
+ et al

[No authors listed]

Author information
  • 1 Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
  • 2 Laboratory for RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
  • 3 Laboratory for RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. Electronic address: markus.landthaler@mdc-berlin.de.
  • 4 Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. Electronic address: rajewsky@mdc-berlin.de.

摘要


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.

原始数据


 保存测序数据
Sample name
Organism Experiment title Sample type Library instrument Attributes
cell linedevelopment stagegenotypeknockdownsource namestraintransfection
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