Journal
RNA BIOLOGY
Volume 9, Issue 11, Pages 1370-1379Publisher
TAYLOR & FRANCIS INC
DOI: 10.4161/rna.22360
Keywords
nonsense-mediated mRNA decay; RNA decay; UPF1; RNA-seq; BRIC-seq
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Funding
- Takeda Science Foundation
- Naito Foundation
- Japan Society for the Promotion of Science
- Funding Program for World-Leading Innovative R&D on Science and Technology of the Japan Society for the Promotion of Science
- Ministry of Education, Culture, Sports, Science and Technology of Japan
- Grants-in-Aid for Scientific Research [221S0002] Funding Source: KAKEN
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UPF1 eliminates aberrant mRNAs harboring premature termination codons, and regulates the steady-state levels of normal physiological mRNAs. Although genome-wide studies of UPF1 targets performed, previous studies did not distinguish indirect UPF1 targets because they could not determine UPF1-dependent altered RNA stabilities. Here, we measured the decay rates of the whole transcriptome in UPF1-depleted HeLa cells using BRIC-seq, an inhibitor-free method for directly measuring RNA stability. We determined the half-lives and expression levels of 9,229 transcripts. 785 transcripts were stabilized in UPF1-depleted cells. Among these, the expression levels of 76 transcripts were increased, but those of the other 709 transcripts were not altered. RNA immunoprecipitation showed UPF1 bound to the stabilized transcripts, suggesting that UPF1 directly degrades the 709 transcripts. Many UPF1 targets in this study were newly identified. This study clearly demonstrates that direct determination of RNA stability is a powerful approach for identifying targets of RNA degradation factors.
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