|
| Status |
Public on Mar 18, 2015 |
| Title |
Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation [icSHAPE] |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
Visualizing the physical basis for molecular behavior inside living cells is a grand challenge in biology. RNAs are central to biological regulation, and RNA’s ability to adopt specific structures intimately controls every step of the gene expression program.1 However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles predominantly viewed only two of four nucleotides that make up RNA.2,3 Here we present a novel biochemical approach, In Vivo Click SHAPE (icSHAPE), that enables the first global view of RNA secondary structures of all four bases in living cells. icSHAPE of embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguishes different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved in vitro, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA binding or modification proteins that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N6-methyladenosine (m6A) modification genome-wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.
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| |
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| Overall design |
Development and implementation of a chemoaffinity method to study the in vivo secondary structure of the transcriptome
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| |
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| Contributor(s) |
Spitale RC, Flynn RA, Zhang QC, Kuchelmeister HY, Crisalli P, Torre EA, Batista PJ, Kool ET, Chang HY |
| Citation(s) |
25799993 |
| |
| Submission date |
Aug 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
380 Roth Way, Room 265
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (10)
|
| GSM1464037 |
v65 polyA(+) icSHAPE DMSO Biological Replicate 1 |
| GSM1464038 |
v65 polyA(+) icSHAPE DMSO Biological Replicate 2 |
| GSM1464039 |
v65 polyA(+) icSHAPE in vitro NAI-N3 Biological Replicate 1 |
| GSM1464040 |
v65 polyA(+) icSHAPE in vitro NAI-N3 Biological Replicate 2 |
| GSM1464041 |
v65 polyA(+) icSHAPE in vivo NAI-N3 Biological Replicate 1 |
| GSM1464042 |
v65 polyA(+) icSHAPE in vivo NAI-N3 Biological Replicate 2 |
| GSM1565484 |
METTL3 KO polyA(+) icSHAPE DMSO Biological Replicate 1 |
| GSM1565485 |
METTL3 KO polyA(+) icSHAPE DMSO Biological Replicate 2 |
| GSM1565486 |
METTL3 KO polyA(+) icSHAPE NAI-N3 Biological Replicate 1 |
| GSM1565487 |
METTL3 KO polyA(+) icSHAPE NAI-N3 Biological Replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE64169 |
Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation |
|
| Relations |
| BioProject |
PRJNA257310 |
| SRA |
SRP045191 |
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