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Series GSE63435 Query DataSets for GSE63435
Status Public on Nov 20, 2014
Title A variety of Dicer substrates in human and C. elegans (CEL RNA-seq)
Organism Caenorhabditis elegans
Experiment type Expression 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 Regulatory impact of Dicer binding was assessed by knock down experiments in human HEK293 cells and Caenorhabditis elegans. Drosha knockdown and mock transfections were used as controls. In total 6 samples (3 human, 3 nematode)
 
Contributor(s) Rybak-Wolf A, Jens M, Murakawa Y, Landthaler M, Rajewsky N
Citation(s) 25416952
Submission date Nov 18, 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)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
Samples (3)
GSM1548737 cel_mock_4
GSM1548738 cel_dcr1_4
GSM1548739 cel_drsh1_4
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 PRJNA267831
SRA SRP050039

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE63435_RAW.tar 480.0 Kb (http)(custom) TAR (of TXT)
GSE63435_sanger_gene.htseq.counts.txt.gz 133.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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