GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE44378 Query DataSets for GSE44378
Status Public on Jul 15, 2013
Title Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates (part 3)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary When adapting to environmental stress, cells attenuate and reprogram their translational output. In part, these altered translation profiles are established through changes in the interactions between RNA-binding proteins and mRNAs. The Ago2/microRNA machinery has been shown to participate in stress-induced translational upregulation of a particular mRNA, CAT-1; however, a detailed, transcriptome-wide understanding of the involvement of Ago2 in the process has been lacking. Here, we profiled the overall changes in Ago2-mRNA interactions upon arsenite stress by CLIP-seq. Ago2 displayed a significant remodeling of its transcript occupancy, with the majority of 3` UTR and CDS sites exhibiting stronger interaction. Interestingly, target sites that were destined for release from Ago2 upon stress were depleted in miRNA complementarity signatures, suggesting an alternative mode of interaction. To compare the changes in Ago2 binding patterns across transcripts with changes in their translational states, we measured mRNA profiles on ribosome/polysome gradients by RNA-seq. Increased Ago2 occupancy correlated with stronger repression of translation for those mRNAs, as evidenced by a shift toward lighter gradient fractions upon stress, while release of Ago2 was associated with the limited number of transcripts that remained translated. Taken together, these data point to a role for Ago2 and the mammalian microRNAs in mediating the translational component of the stress response.
Overall design In this sub-series, CLIP and RNAseq data from the hippuristanol treatment experiment are presented. Experiments on 293S cells +/- hippuristanol treatment, in 2 biological replicates. Here, for each treatment/replicate sample, an aliquot was used for RNA-seq, and the rest was split into three aliquots to perform 3 parallel CLIP-seq protocols with different antibodies. So, each RNA-seq dataset here corresponds to 3 CLIP-seq datasets.
Contributor(s) Karginov FV, Hannon GJ
Citation(s) 23824327
Submission date Feb 18, 2013
Last update date Mar 04, 2023
Contact name Fedor Karginov
Organization name UC Riverside
Department MCSB
Street address 900 University Ave
City Riverside
State/province California
ZIP/Postal code 92521
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (16)
GSM1084072 CLIP_nohippuristanol_rep1_AbnovaAb
GSM1084073 CLIP_hippuristanol_rep1_AbnovaAb
GSM1084074 CLIP_nohippuristanol_rep1_SantaCruzAb
This SubSeries is part of SuperSeries:
GSE44404 Remodeling of Ago2-mRNA interactions upon cellular stress reflects miRNA complementarity and correlates with altered translation rates
BioProject PRJNA189782
SRA SRP018718

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
GSE44378_hipp_nohipp_CLIP_peak_abundances.txt.gz 152.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap