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Series GSE47078 Query DataSets for GSE47078
Status Public on Jul 20, 2015
Title RC3H1 posttranscriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kB pathway [PARCLIP]
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFalpha mRNA decay via a 3'UTR constitutive decay element (CDE). Here, we applied PAR-CLIP to human RC3H1 to identify about 3800 mRNA targets with more than 16000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins. RC3H1 binds preferentially short-lived and DNA damage induced mRNAs, indicating a role of this RNA-binding protein in the posttranscriptional regulation of the DNA damage response. Intriguingly, RC3H1 affects expression of NF-kB pathway regulators such as IkBalpha and A20. RC3H1 uses roquin and Zn-finger domains to contact a binding site in the A20 3'UTR, demonstrating a not yet recognized mode of RC3H1 binding. Knockdown of RC3H1 resulted in increased A20 protein expression, thereby interfering with IkB kinase and NF-kB activities, demonstrating that RC3H1 can modulate the activity of the IKK/NF-kB pathway.
 
Overall design One PAR-CLIP Sample with human HEK293 cells
 
Contributor(s) Murakawa Y, Landthaler M
Citation(s) 26170170
Submission date May 18, 2013
Last update date May 15, 2019
Contact name Markus Landthaler
E-mail(s) markus.landthaler@mdc-berlin.de
Phone +49-30-9406-3026
Organization name Max-Delbrück-Center for Molecular Medicine
Department Berlin Institute for Medical Systems Biology
Street address Robert-Rössle-Straße 10
City Berlin
ZIP/Postal code 13125
Country Germany
 
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (1)
GSM1144507 RC3H1_PARCLIP
This SubSeries is part of SuperSeries:
GSE69153 RC3H1 posttranscriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kB pathway
Relations
BioProject PRJNA203446
SRA SRP022892

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE47078_RAW.tar 310.0 Kb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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