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Series GSE63458 Query DataSets for GSE63458
Status Public on Nov 20, 2014
Title A variety of Dicer substrates in human and C. elegans (HEK small RNA)
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary 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.
 
Overall design small RNAs were extracted from total RNA. Standard small RNA sequencing was performed to sequence 5' monophosphate bearing small RNAs. This was performed for siRNA knockdowns of DICER1 or DROSHA, with two independent siRNAs each, and for control cells. (5 samples in total)
 
Contributor(s) Rybak-Wolf A, Jens M, Murakawa Y, Landthaler M, Rajewsky N
Citation(s) 25416952
Submission date Nov 19, 2014
Last update date May 15, 2019
Contact name Marvin Jens
E-mail(s) marvin.jens@mdc-berlin.de
Phone +493094062989
Organization name Max Delbrueck Center for Molecular Medicine
Department Systems Biology of Gene Regulatory Elements
Lab Rajewsky lab
Street address Robert Rössle Str. 10 (H. 87)
City Berlin
ZIP/Postal code 13092
Country Germany
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (5)
GSM1550165 negative control
GSM1550166 DICER1 KD siRNA1
GSM1550167 DICER1 KD siRNA2
This SubSeries is part of SuperSeries:
GSE55333 Transcriptome wide identification of Dicer binding in human and C. elegans reveals a variety of substrates
Relations
BioProject PRJNA267838
SRA SRP050042

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE63458_RAW.tar 25.9 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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