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| Status |
Public on Jul 23, 2012 |
| Title |
Genome-wide analysis of cellular NMD substrates that regulated by Upf1, PNRC2 or CTIF in HeLa cell |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Third-party reanalysis
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| Summary |
The first round of translation occurs on mRNAs bound by nuclear cap-binding complex (CBC), which is composed of nuclear cap-binding protein (CBP) 80 and 20. During this round of translation, aberrant mRNAs are recognized and downregulated in abundance by nonsense-mediated mRNA decay (NMD), which is one of the mRNA quality control mechanisms. Here our microarray analysis reveals that the level of cyclin-dependent kinase inhibitor 1A (CDKN1A) mRNAs increases in the cells depleted of cellular NMD factors. Intriguingly, CDKN1A mRNA contains an upstream open reading frame (uORF), which is one of NMD-inducing features. Using chimeric reporter constructs and confocal microscopy, we find that the uORF of CDKN1A mRNA is actively translated and modulates a translational efficiency of the main downstream ORF. Our findings provide the biological insights into the possible role of NMD in diverse pathways mediated by CDKN1A. The microarray analysis performed to analize the cellular NMD substrates that regulated by Upf1, PNRC2 and/or CTIF in HeLa cell. The hypothesis tested in the present study was that endogenous NMD substrates may co-regulated by Upf1, PNRC2 and CTIF. Results provide important information that vast range of cellular NMD substrates are reqired CTIF.
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| Overall design |
Total RNA obtained from HeLa cells with downregulation of Upf1, PNRC2 or CTIF by siRNA. The up- or down-regulated transcripts were compare to control siRNA treated HeLa cell RNA extract. Significant transcripts were confirmed by replication.
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| Contributor(s) |
Kim KM, Cho H |
| Citation(s) |
22771799 |
| Submission date |
Apr 24, 2012 |
| Last update date |
Mar 20, 2017 |
| Contact name |
Kyoung Mi Kim |
| E-mail(s) |
naragu47@korea.ac.kr
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| Organization name |
Korea University
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| Department |
School of Life sciences and biotechnology
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| Lab |
RNA genomics
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| Street address |
Anam-Dong
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| City |
Seoul |
| ZIP/Postal code |
136-701 |
| Country |
South Korea |
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| Platforms (1) |
| GPL6883 |
Illumina HumanRef-8 v3.0 expression beadchip |
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| Samples (2) |
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| Relations |
| Reanalysis of |
GSM659011 |
| Reanalysis of |
GSM659012 |
| Reanalysis of |
GSM659013 |
| Reanalysis of |
GSM659014 |
| Reanalysis of |
GSM659015 |
| Reanalysis of |
GSM659010 |
| BioProject |
PRJNA161531 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37538_RAW.tar |
3.9 Mb |
(http)(custom) |
TAR |
| GSE37538_non-normalized.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE37538_normalized.txt.gz |
229.2 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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