Solomon et al. 2017 (PRJNA391171)
General Details
| Title | RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA Secondary Structure |
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| Organism | |
| Number of Samples | 2 |
| Release Date | 2017/06/19 00:00 |
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Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP109827 |
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| ENA | SRP109827 |
| GEO | GSE100210 |
| BioProject | PRJNA391171 |
Publication
| Title | |
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| Authors | Solomon O, Di Segni A, Cesarkas K, Porath HT, Marcu-Malina V, Mizrahi O, Stern-Ginossar N, Kol N, Farage-Barhom S, Glick-Saar E, Lerenthal Y, Levanon EY, Amariglio N, Unger R, Goldstein I, Eyal E, Rechavi G |
| Journal | Nature communications |
| Publication Date | 2017 Nov 13 |
| Abstract | Adenosine deaminase acting on RNA 1 (ADAR1) is the master RNA editor, catalyzing the deamination of adenosine to inosine. RNA editing is vital for preventing abnormal activation of cytosolic nucleic acid sensing pathways by self-double-stranded RNAs. Here we determine, by parallel analysis of RNA secondary structure sequencing (PARS-seq), the global RNA secondary structure changes in ADAR1 deficient cells. Surprisingly, ADAR1 silencing resulted in a lower global double-stranded to single-stranded RNA ratio, suggesting that A-to-I editing can stabilize a large subset of imperfect RNA duplexes. The duplexes destabilized by editing are composed of vastly complementary inverted Alus found in untranslated regions of genes performing vital biological processes, including housekeeping functions and type-I interferon responses. They are predominantly cytoplasmic and generally demonstrate higher ribosomal occupancy. Our findings imply that the editing effect on RNA secondary structure is context dependent and underline the intricate regulatory role of ADAR1 on global RNA secondary structure. |
| PMC | PMC5682290 |
| PMID | 29129909 |
| 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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| SRR5720008 | PRJNA391171 | Homo sapiens | HepG2 | Ribo-Seq | 0.0 |  |
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| SRR5720009 | PRJNA391171 | Homo sapiens | HepG2 | Ribo-Seq | 0.0 | |
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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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