 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 21, 2012 |
| Title |
The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis |
| Organism |
Schizosaccharomyces pombe |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Homeostatic control mechanisms are essentil to life. One such mechanism, the unfolded protein response (UPR) operates in all eukarytic cells to adjust protein folding capacity of the endoplasmic reticulum (ER) according to need. UPR induction in all eurkarytic cells to date involves Ire1 (kinase/endonuclease transmembrane protein) mediated a non-convential splicing of Hac1/XBP1 mRNA, encoding for a potent transcription factor. UPR induction causes a comprehensive transcriptional upregulation of the folding capacity in the ER. Here we studied the global transcriptional profile of the UPR in fission yeast. Fission yeast lacks a clear homolog of Hac1/XBP1. Instead Ire1 maintains ER homeostasis through two post-transciptional programs: selective mRNA decay and processing of Bip1 mRNA (encoding for a major HS70-familiy member in the ER) thereby stabilizing it.
|
| |
|
| Overall design |
S. pombe cells were grown in liquid medium (YE5S) to OD600=0.25. Cells were treated with or without 2 mM DTT (Dithiothreitol, impairs disulfid bond formation) for 60 min at 30℃. Total RNA was extracted from cells using hot phenol method. PolyA+ mRNA were enriched by two sequential rounds of oligo-dT (Invitrogen) selection. rRNA depletion was performed by depletion of ll RNA smaller than 200nt (mirVana miRNA Purification Kit (Ambion) followed by two rounds of subtractive hybridization using Ribominus EukaryoteKit for RNA-seq (Invitrogen). To sequence 2',3'-cyclic phosphate cleavage products tRNA ligase was used to selectively ligate an RNA linker to all 2',3'-cyclic phosphatesin total RNA. (described in Schutz et al., 2010). Two biological repeats were performed for the following samples with different conditions and yeast strains: poly A+ mRNA sample and mRNA enriched (ribosome depletion). On replicate was performed for RNA 3' end mapping carrying a 2',3'-cyclic phosphate: 1 replicate
|
| |
|
| Contributor(s) |
Kimmig P, Diaz M, Lang A, Zheng J, Williams C, Aragón T, Li H, Walter P |
| Citation(s) |
23066505 |
| |
| Submission date |
Aug 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Philipp Kimmig |
| Organization name |
University of California, San Francisco
|
| Department |
Biochemistry and Biophysics
|
| Lab |
Peter Walter lab
|
| Street address |
Genentech Hall N316, 600 16th Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158-2517 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL9453 |
Illumina Genome Analyzer II (Schizosaccharomyces pombe) |
| GPL13988 |
Illumina HiSeq 2000 (Schizosaccharomyces pombe) |
|
| Samples (15)
|
| GSM991008 |
polyA+ enriched mRNA, WT -DTT Rep 1 |
| GSM991009 |
polyA+ enriched mRNA, WT +DTT Rep 1 |
| GSM991010 |
polyA+ enriched mRNA, Ire1Δ +DTT Rep 1 |
| GSM991011 |
polyA+ enriched mRNA, WT -DTT Rep 2 |
| GSM991012 |
polyA+ enriched mRNA, WT +DTT Rep 2 |
| GSM991013 |
polyA+ enriched mRNA, Ire1Δ +DTT Rep 2 |
| GSM991014 |
mRNA enriched, WT -DTT Rep 1 (rRNA depleted) |
| GSM991015 |
mRNA enriched, WT +DTT Rep 1 (rRNA depleted) |
| GSM991016 |
mRNA enriched, WT -DTT Rep 2 (rRNA depleted) |
| GSM991017 |
mRNA enriched, WT +DTT Rep 2 (rRNA depleted) |
| GSM991018 |
mRNA enriched, ire1Δ +DTT (rRNA depleted) |
| GSM991019 |
2',3'-cyclic phosphate-terminated RNA, Ski2Δ +DTT Technical Rep 1 |
| GSM991020 |
2',3'-cyclic phosphate-terminated RNA Ire1Δ/Ski2Δ +DTT Technical Rep1 |
| GSM991021 |
2',3'-cyclic phosphate-terminated RNA, Ski2Δ +DTT Technical Rep 2 |
| GSM991022 |
2',3'-cyclic phosphate-terminated RNA Ire1Δ/Ski2Δ +DTT Technical Rep2 |
|
| Relations |
| BioProject |
PRJNA173435 |
| SRA |
SRP015005 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40298_RAW.tar |
100.7 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...