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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 23, 2015 |
| Title |
Systematic discovery of cap-independent translation sequences in human and viral genomes |
| Organism |
synthetic construct |
| Experiment type |
Other
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| Summary |
To investigate gene specificity at the level of translation in both the human genome and viruses, we devised a high-throughput bicistronic assay to quantify cap-independent translation. We uncovered thousands of novel cap-independent translation sequences, and we provide insights on the landscape of translational regulation in both humans and viruses. We find extensive translational elements in the 3′ untranslated region of human transcripts and the polyprotein region of uncapped RNA viruses. Through the characterization of regulatory elements underlying cap-independent translation activity, we identify potential mechanisms of secondary structure, short sequence motif,and base pairing with the 18S ribosomal RNA (rRNA). Furthermore, we systematically map the 18S rRNA regions for which reverse complementarity enhances translation. Thus, we make available insights into the mechanisms of translational control in humans and viruses.
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| Overall design |
high-throughput bicistronic assay for obtaining cap-independent translation measurements of 55,000 fully designed sequences in parallel using fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq).
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| Contributor(s) |
Weingarten-Gabbay S, Elias-Kirma S, Nir R, Gritsenko AA, Stern-Ginossar N, Yakhini Z, Weinberger A, Segal E |
| Citation(s) |
26816383 |
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| Submission date |
Oct 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shira Weingarten-Gabbay |
| Organization name |
The Broad Institute
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| Street address |
75 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platforms (2) |
| GPL15228 |
Illumina HiSeq 2000 (synthetic construct) |
| GPL17769 |
Illumina MiSeq (synthetic construct) |
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| Samples (6)
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| GSM1916137 |
pEF1-mRFP-oligos-eGFP library 16 expression Bins |
| GSM1916138 |
pEF1-mRFP-oligos-eGFP library total |
| GSM1916139 |
pEF1del-mRFP-oligos-eGFP library eGFP positive population |
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| Relations |
| BioProject |
PRJNA299626 |
| SRA |
SRP065210 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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