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| Status |
Public on Jul 23, 2021 |
| Title |
Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes Identifies Dynamic Changes During Mammalian Erythropoiesis (mRNA) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Two features of eukaryotic RNA molecules that regulate their post-transcriptional fates are RNA secondary structure and RNA-binding protein (RBP) interaction sites. However, a comprehensive global overview of the dynamic nature of these sequence features during erythropoiesis has never been obtained. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approach to reveal the global landscape of RNA secondary structure and RBP-RNA interaction sites and the dynamics of these features during this important developmental process. We identify dynamic patterns of RNA secondary structure and RBP binding that are consistently anti-correlated throughout mRNAs during erythropoiesis. Additionally, we determine a set of protein-bound sequence motifs and their dynamic structural and RBP binding contexts. Finally, using these dynamically bound sequences, we identify a number of RBPs that have known and putative key functions in post-transcriptional regulation during mammalian erythropoiesis. In total, this global analysis reveals new post-transcriptional regulators of mammalian blood cell development.
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| Overall design |
mRNA-seq of 2 biological replicates of MEL cells at day 0, day 2, and day 4 post differentiation induction by DMSO
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| Contributor(s) |
Shan M, Ji X, Janssen K, Silverman IM, Humenik J, Garcia BA, Liebhaber SA, Gregory BD |
| Citation(s) |
34315813 |
| Submission date |
Apr 09, 2020 |
| Last update date |
Aug 11, 2021 |
| Contact name |
Mengge Shan |
| E-mail(s) |
mengge@pennmedicine.upenn.edu
|
| 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) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA624166 |
| SRA |
SRP255908 |
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