Lu et al. 2019 (PRJNA316125)
General Details
| Title | Finding new proteins encoded by long non-coding RNAs in human cells |
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| Organism | |
| Number of Samples | 3 |
| Release Date | 2016/03/23 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP072231 |
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| ENA | SRP072231 |
| GEO | GSE79539 |
| BioProject | PRJNA316125 |
Publication
| Title | |
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| Authors | Lu S, Zhang J, Lian X, Sun L, Meng K, Chen Y, Sun Z, Yin X, Li Y, Zhao J, Wang T, Zhang G, He QY |
| Journal | Nucleic acids research |
| Publication Date | 2019 Sep 5 |
| Abstract | It has been a long debate whether the 98% 'non-coding' fraction of human genome can encode functional proteins besides short peptides. With full-length translating mRNA sequencing and ribosome profiling, we found that up to 3330 long non-coding RNAs (lncRNAs) were bound to ribosomes with active translation elongation. With shotgun proteomics, 308 lncRNA-encoded new proteins were detected. A total of 207 unique peptides of these new proteins were verified by multiple reaction monitoring (MRM) and/or parallel reaction monitoring (PRM); and 10 new proteins were verified by immunoblotting. We found that these new proteins deviated from the canonical proteins with various physical and chemical properties, and emerged mostly in primates during evolution. We further deduced the protein functions by the assays of translation efficiency, RNA folding and intracellular localizations. As the new protein UBAP1-AST6 is localized in the nucleoli and is preferentially expressed by lung cancer cell lines, we biologically verified that it has a function associated with cell proliferation. In sum, we experimentally evidenced a hidden human functional proteome encoded by purported lncRNAs, suggesting a resource for annotating new human proteins. © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| PMC | PMC6735797 |
| PMID | 31340039 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR3286543 | PRJNA316125 | Homo sapiens | HBE | Ribo-Seq | Cycloheximide |  |
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| SRR3286544 | PRJNA316125 | Homo sapiens | A549 | Ribo-Seq | Cycloheximide | |
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| SRR3286545 | PRJNA316125 | Homo sapiens | H1299 | Ribo-Seq | Cycloheximide | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
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