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| Status |
Public on Jun 15, 2022 |
| Title |
Global analysis reveals large scale dynamics of protein-RNA interaction and RNA secondary structure characteristics of Physcomitrella patens ABA response (mRNA) |
| Organism |
Physcomitrium patens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Eukaryotic RNA molecules undergo multiple regulatory steps prior to being translated as proteins. Two features of post-transcriptional regulation are RNA secondary structure and RNA-binding protein (RBP) interactions with mRNAs. Here we reveal the global landscape of RBP-RNA interactions the bryophyte Physcomitrella patens undergoes as part of its response to the phytohormone abscisic acid (ABA). We show that P. patens undergoes large scale shifts in RNA secondary structure and RBP-RNA interactions as well as identify sites of RBP-RNA interaction and describe enriched motifs, among which are two purine rich sequences. We further elucidate the collection of proteins that bind to these sequences, among which are P. patens cold shock containing proteins. Together, the data suggest that P. patens undergoes a large-scale change in RNA secondary structure and RBP binding as a response to ABA and also identifies CSPs as well as several other proteins as possible regulators of that response.
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| Overall design |
mRNA-seq of 2 biological replicates of P. patens protonema treated with 10 uM ABA for 0, 30, or 60 minutes
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| Contributor(s) |
Shan M, Willmann MR, Gregory BD |
| Citation missing |
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| |
| Submission date |
Apr 09, 2020 |
| Last update date |
Jun 16, 2022 |
| Contact name |
Mengge Shan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennylsvania
|
| Department |
Biology
|
| Lab |
Brian Gregory
|
| Street address |
433 South University Avenue
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL17793 |
Illumina HiSeq 2500 (Physcomitrella patens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA624165 |
| SRA |
SRP255909 |
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