Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability.
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. An amount of 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.
Radioisotope Center, University of Tokyo, Tokyo, Japan.
Hidenori
H
Tani
Naoto
N
Imamachi
Kazi Abdus
KA
Salam
Rena
R
Mizutani
Kenichi
K
Ijiri
Takuma
T
Irie
Tetsushi
T
Yada
Yutaka
Y
Suzuki
Nobuyoshi
N
Akimitsu
D045744:Cell Line, Tumor; D018389:Codon, Nonsense; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020365:RNA Helicases; D034622:RNA Interference; D020871:RNA Stability; D012333:RNA, Messenger / Q000235:genetics*; D034741:RNA, Small Interfering; D017423:Sequence Analysis, RNA; D015534:Trans-Activators / Q000235:genetics* / Q000378:metabolism*; D059467:Transcriptome
D018389:Codon, Nonsense; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D015534:Trans-Activators; D020365:RNA Helicases; C101828:UPF1 protein, human