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| Status |
Public on May 01, 2013 |
| Title |
Cold induced RNA-binding proteins influence alternative polyadenylation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
We employed PAR-CLIP, a recently developed method based on RNA-protein crosslinking, to identify Cirbp and Rbm3 binding sites at transcriptome-level. Genome-wide RNA-seq analysis indicated that cold temperature leads to extensive 3’UTR lengthening whereas the loss of Cirbp or Rbm3 resulted in 3’UTR shortening. Combining with PAR-CLIP results, we found that these two RBPs repress the polyadenylation adjacent to their binding sites.
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| Overall design |
Examination of the binding sites of Cirbp and Rbm3 by PAR-CLIP and their influence on the transcriptome by RNA-seq. PARCLIP was performed as in Hafner et al. 2010 Cell 141, 129–141, with MEFs cell lines stably expressing FLAG-tagged Cirbp and Rbm3. We used 4-thiouridine (4SU) to enhance the crosslink. For RNA-seq, polyadenylated RNA from the mock-transfected cells at 37°C or 32°C with two replicates, siCirbp-1, siCirbp-2, siRbm3-1 and siRbm3-2 MEFs at 37°C were sequenced on Solexa GAII using 76bp single-end kits according to the manufacturer’s instructions.
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| Contributor(s) |
Liu Y, Yan J |
| Citation(s) |
23792593 |
| Submission date |
Aug 29, 2012 |
| Last update date |
Feb 07, 2020 |
| Contact name |
Yuting Liu |
| E-mail(s) |
ytliu@picb.ac.cn
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| Phone |
02154920548
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| Organization name |
PICB
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| Department |
Functional Genomics
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| Lab |
Functional Genomics
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| Street address |
YueyangRoad320
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| City |
Shanghai |
| State/province |
- |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA174190 |
| SRA |
SRP015331 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40468_RAW.tar |
8.0 Mb |
(http)(custom) |
TAR (of BED, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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