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| Status |
Public on Jun 17, 2016 |
| Title |
RNA-seq of hESC samples upon loss of UPF1. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Nonsense-mediated RNA decay (NMD) is a highly conserved pathway that selectively degrades specific subsets of RNA transcripts. Here, we provide evidence that NMD regulates early human developmental cell fate. We found that NMD factors tend to be expressed at higher levels in human pluripotent cells than differentiated cells, raising the possibility that NMD must be downregulated to permit differentiation. Loss- and gain-of-function experiments in human embryonic stem cells (hESCs) demonstrated that, indeed, NMD downregulation is essential for efficient generation of definitive endoderm. RNA-seq analysis identified NMD target transcripts induced when NMD is suppressed in hESCs, including many encoding signaling components. This led us to test the role of TGF-b and BMP signaling, which we found NMD acts through to influence definitive endoderm vs. mesoderm fate. Our results suggest that selective RNA decay is critical for specifying the developmental fate of specific human embryonic cell lineages.
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| |
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| Overall design |
Examination of differential gene expression in hESCs upon loss of UPF1.
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| |
|
| Contributor(s) |
Lou C, Chousal J |
| Citation(s) |
27304915 |
| |
| Submission date |
May 06, 2016 |
| Last update date |
Sep 15, 2022 |
| Contact name |
Heidi Cook-Andersen |
| E-mail(s) |
hcookandersen@ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Department |
Department of Reproductive Medicine
|
| Street address |
2880 Torrey Pines Scenic Drive, Rm 4811
|
| City |
La Jolla |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (4)
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| Relations |
| BioProject |
PRJNA320895 |
| SRA |
SRP074494 |
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