Jackson et al. 2018 (PRJNA494404)
General Details
| Title | The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity |
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| Organism | |
| Number of Samples | 10 |
| Release Date | 2018/10/02 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP163147 |
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| ENA | SRP163147 |
| GEO | GSE120762 |
| BioProject | PRJNA494404 |
Publication
| Title | |
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| Authors | Jackson R,Kroehling L,Khitun A,Bailis W,Jarret A,York AG,Khan OM,Brewer JR,Skadow MH,Duizer C,Harman CCD,Chang L,Bielecki P,Solis AG,Steach HR,Slavoff S,Flavell RA |
| Journal | Nature |
| Publication Date | 2018 Dec |
| Abstract | The annotation of the mammalian protein-coding genome is incomplete. Arbitrary size restriction of open reading frames (ORFs) and the absolute requirement for a methionine codon as the sole initiator of translation have constrained the identification of potentially important transcripts with non-canonical protein-coding potential 1,2 . Here, using unbiased transcriptomic approaches in macrophages that respond to bacterial infection, we show that ribosomes associate with a large number of RNAs that were previously annotated as 'non-protein coding'. Although the idea that such non-canonical ORFs can encode functional proteins is controversial 3,4 , we identify a range of short and non-ATG-initiated ORFs that can generate stable and spatially distinct proteins. Notably, we show that the translation of a new ORF 'hidden' within the long non-coding RNA Aw112010 is essential for the orchestration of mucosal immunity during both bacterial infection and colitis. This work expands our interpretation of the protein-coding genome and demonstrates that proteinaceous products generated from non-canonical ORFs are crucial for the immune response in vivo. We therefore propose that the misannotation of non-canonical ORF-containing genes as non-coding RNAs may obscure the essential role of a multitude of previously undiscovered protein-coding genes in immunity and disease. |
| PMC | PMC6939389 |
| PMID | 30542152 |
| 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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| SRR7956044 | PRJNA494404 | Mus musculus | Macrophage | RiboTag |  |
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| SRR7956045 | PRJNA494404 | Mus musculus | Macrophage | RiboTag | |
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| SRR7956046 | PRJNA494404 | Mus musculus | Macrophage | RiboTag | |
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| SRR7956047 | PRJNA494404 | Mus musculus | Macrophage | RiboTag | |
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| SRR7956048 | PRJNA494404 | Mus musculus | Macrophage | RiboTag | |
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| SRR7956049 | PRJNA494404 | Mus musculus | Macrophage | RiboTag | |
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| SRR7956050 | PRJNA494404 | Mus musculus | Macrophage | Ribo-Seq | Cycloheximide | |
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| SRR7956051 | PRJNA494404 | Mus musculus | Macrophage | Ribo-Seq | Cycloheximide | |
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| SRR7956052 | PRJNA494404 | Mus musculus | Macrophage | Ribo-Seq | Cycloheximide | |
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| SRR7956053 | PRJNA494404 | Mus musculus | Macrophage | 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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